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https://en.wikipedia.org/wiki/Enterovirus%205%E2%80%B2%20cloverleaf%20cis-acting%20replication%20element | The Enterovirus 5′ cloverleaf cis-acting replication element is an RNA element found in the 5′ UTR of Enterovirus genomes. The element has a cloverleaf like secondary structure and is known to be a multifunctional cis-acting replication element (CRE), required for the initiation of negative strand RNA synthesis.
See also
Enteroviral 3′ UTR element
Enterovirus cis-acting replication element
References
External links
Cis-regulatory RNA elements
Enteroviruses |
https://en.wikipedia.org/wiki/CsrB/RsmB%20RNA%20family | The CsrB RNA is a non-coding RNA that binds to approximately 9 to 10 dimers of the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia carotovora the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
RsmB RNA was shown to be upregulated by GacS/A system, and increase downstream T3SS gene expression. FlhDC, the master regulator of flagellar genes, also activates rsmB RNA production. A regulatory network have been revealed connecting rsmB, FlhDC and T3SS.
It has been shown to play role in the biocontrol activity of Rahnella aquatilis HX2 (a biocontrol agent producing antibacterial substance).
See also
CsrC RNA family
PrrB/RsmZ RNA family
RsmY RNA family
RsmX
RsmW sRNA
CsrA protein
References
External links
Pfam page for the CsrA protein family
Non-coding RNA |
https://en.wikipedia.org/wiki/Enterovirus%20cis-acting%20replication%20element | Enterovirus cis-acting replication element is a small RNA hairpin in the coding region of protein 2C as the site in PV1(M) RNA that is used as the primary template for the in vitro uridylylation. The first step in the replication of the plus-stranded poliovirus RNA is the synthesis of a complementary minus strand. This process is initiated by the covalent attachment of uridine monophosphate (UMP) to the terminal protein VPg, yielding VPgpU and VPgpUpU.
See also
Enteroviral 3′ UTR element
Enterovirus 5′ cloverleaf cis-acting replication element
References
External links
Cis-regulatory RNA elements
Enteroviruses |
https://en.wikipedia.org/wiki/Equine%20arteritis%20virus%20leader%20TRS%20hairpin%20%28LTH%29 | The equine arteritis virus leader transcription-regulating sequence hairpin (LTH) is as RNA element that is thought to be a key structural element in discontinuous subgenomic RNA synthesis and is critical for leader transcription-regulating sequences (TRS) function. Similar structures have been predicted in other arteriviruses and coronaviruses.
References
External links
Cis-regulatory RNA elements
Arteriviridae |
https://en.wikipedia.org/wiki/FGF-1%20internal%20ribosome%20entry%20site%20%28IRES%29 | The FGF-1 internal ribosome entry site (IRES) is an RNA element present in the 5' UTR of the mRNA of fibroblast growth factor-1 and allows cap-independent translation. It is thought that FGF-1 internal ribosome entry site (IRES) activity is strictly controlled and highly tissue specific.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/FGF-2%20internal%20ribosome%20entry%20site%20%28IRES%29 | The FGF-2 internal ribosome entry site is an RNA element present in the 5' UTR of the mRNA of fibroblast growth factor-2. It has been found that the FGF-2 internal ribosome entry site (IRES) activity is strictly controlled and highly tissue specific. It is thought that translational IRES dependent activation of FGF-2 plays a vital role in embryogenesis and in the adult brain [1]. When expressed the fibroblast growth factor 2 FGF-2 protein plays a pivotal role in cell proliferation, differentiation and survival as well as being involved in wound-healing [1,2].
References
Further reading
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Ctgf/hcs24%20CAESAR | ctgf/hcs24 CAESAR is the name given to the cis-acting RNA element identified in the 3' untranslated region (3'UTR) of the human connective tissue growth factor (CTGF) messenger RNA. This gene is also known as hypertrophic chondrocyte specific 24 (hcs24).
The importance of the 3'UTR in repressing ctgf gene expression was initially characacterised and subsequently the minimal RNA element responsible for repression was identified This element was predicted to form a stable secondary structure, which acts as a post-transcriptional cis-acting element of structure-anchored repression (CAESAR).
The 3'UTR of the ctgf/hcs24 gene in chicken has also been shown to be involved in repression of gene expression.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/FIE3%20%28ftz%20instability%20element%203%E2%80%B2%29%20element | The FIE3 (ftz instability element 3′) element is an RNA element found in the 3′ UTR of the fushi tarazu mRNA.
The fushi tarazu gene is essential for the establishment of the Drosophila embryonic body plan. When first expressed in early embryogenesis, fushi tarazu mRNA is uniformly distributed over most of the embryo. Subsequently, fushi tarazu mRNA expression rapidly evolves into a pattern of seven stripes that encircle the embryo. The instability of fushi tarazu mRNA may contribute to the localization of this pattern of expression, but this is unlikely to be a dominant effect since the 744 base-pair ftz zebra stripe element can drive the ectopic expression of a reporter construct (with mRNA structure entirely unrelated to the ftz transcript) in a qualitatively highly similar pattern. Experiments provide evidence for at least two destabilizing elements in the fushi tarazu mRNA, one located within the 5′ one-third of the mRNA and the other near the 3′ end (termed FIE3 for ftz instability element 3′). The FIE3 lies within a 201-nucleotide sequence just upstream of the polyadenylation signal and can act autonomously to destabilize a heterologous mRNA. Further deletion constructs identified an essential 68-nucleotide element within the FIE3. Although this element is predicted to contain a secondary structure, it also contains a GU rich sequence (UGUUUUGUUU) that is similar to GU rich instability elements subsequently identified in other systems.
References
External links
RN |
https://en.wikipedia.org/wiki/FinP | FinP encodes an antisense non-coding RNA gene that is complementary to part of the TraJ 5' UTR. The FinOP system regulates the transfer of F-like plasmids. The traJ gene encodes a protein required for transcription from the major transfer promoter, pY. The FinO protein is essential for effective repression, acting by binding to FinP and protecting it from RNase E degradation.
References
External links
Antisense RNA |
https://en.wikipedia.org/wiki/FMN%20riboswitch | The FMN riboswitch (also known as RFN element) is a highly conserved RNA element which is naturally occurring, and is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. This element is a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins, thus giving it the ability to regulate RNA expression by responding to changes in the concentration of FMN. In Bacillus subtilis, previous studies have shown that this bacterium utilizes at least two FMN riboswitches, where one controls translation initiation, and the other controls premature transcription termination. Regarding the second riboswitch in Bacilius subtilis, premature transcription termination occurs within the 5' untranslated region of the ribDEAHT operon, precluding access to the ribosome-binding site of ypaA mRNA. FMN riboswitches also have various magnesium and potassium ions dispersed throughout the nucleotide structure, some of which participate in binding of FMN.
In the bacterium Fusobacterium nucleatum, FMN binding has been studied. The FMN riboswitch is able to selectively bind the FMN molecule due to several distinct nucleic acid residues, as well as some of the magnesium ions present in the overall riboswitch structure. FMN's planar isoalloxazine ring system intercalates between A48 and A85 residues on the riboswitch, thereby providing a continuous stacking alignment. Further, the uracil |
https://en.wikipedia.org/wiki/GadY | GadY RNA (previously named IS183 in ) is a non-coding RNA. The GadY gene is located on between and on the opposite strand to the GadX and GadW genes. GadY can form base pairs with the 3' UTR of its target mRNA gadX, this pairing is thought to confer increased stability to the transcript, allowing accumulation of gadX (a transcriptional regulator of the acid response) and therefore increased expression of downstream acid resistance genes. The GadY gene produces three overlapping transcripts that differ in length. The long form is 105 nucleotides in length and two processed versions are 59 and 90 nucleotides in length. It has been shown that all three forms of GadY bind to the Hfq protein.
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/K10%20transport/localisation%20element%20%28TLS%29 | The K10 transport/localisation element (TLS) is a 44 nucleotide K10 TLS regulatory element from Drosophila melanogaster. K10 TLS is responsible for the transport and anterior localisation of K10 mRNA and acts to establish dorsoventral polarity in the oocyte. It was discovered by Julia Serano.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/GAIT%20element | The gamma interferon inhibitor of translation element or GAIT element is a cis-acting RNA element located in the 3'-UTR of the ceruloplasmin (Cp) mRNA.
The GAIT element forms a stem-loop secondary structure. The GAIT element is involved in selective translational silencing of the Cp transcript within monocytic cells, but not hepatic cells. Cp is a multifunctional, copper-containing glycoprotein produced by the liver and secreted into the plasma for its role in copper and iron homeostasis. Ceruloplasmin is also an acute-phase protein produced by monocytes, and its plasma concentration can double during multiple inflammatory conditions through increased Cp production by monocytic cells after stimulation by interferon gamma (IFNγ). Plasma Cp has been reported to be an independent risk factor for cardiovascular disease, including atherosclerosis, carotid restenosis after endarterectomy, and myocardial infarction. Translational silencing of Cp, and possibly other transcripts, mediated by the GAIT element may contribute to the resolution of the local inflammatory response following cytokine activation of macrophages.
The silencing of Cp protein translation in IFN-gamma-stimulated monocytes is accomplished by binding of the IFN-gamma-activated inhibitor of translation (GAIT) inhibitor complex to the GAIT element. The GAIT complex consists of the proteins ribosomal protein L13a, glutamyl-prolyl-tRNA synthetase, NS1-associated protein-1, and glyceraldehyde 3-phosphate dehydrogenase. |
https://en.wikipedia.org/wiki/Gammaretrovirus%20core%20encapsidation%20signal | The Gammaretrovirus core encapsidation signal is an RNA element known to be essential for stable dimerisation and efficient genome packaging during virus assembly. Dimerisation of the viral RNA genomes is proposed to act as an RNA conformational switch which exposes conserved UCUG elements and enables efficient genome encapsidation. The structure of this element is composed of three stem-loops. Two of the stem-loops called SL-C and SL-D form a single co-axial extend helix.
See also
Bacteriophage pRNA
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/G-CSF%20factor%20stem-loop%20destabilising%20element | The G-CSF factor stem-loop destabilising element (SLDE) is an RNA element secreted by fibroblasts and endothelial cells in response to the inflammatory mediators interleukin-1 (IL-1) and tumour necrosis factor-alpha and by activated macrophages. The synthesis of G-CSF is regulated both transcriptionally and through control of mRNA stability. In unstimulated cells G-CSF mRNA is unstable but becomes stabilised in response to IL-1 or tumour necrosis factor alpha, and also in the case of monocytes and macrophages, in response to lipopolysaccharide. It is likely that the presence of the SLDE in the G-CSF mRNA contributes to the specificity of regulation of G-CSF mRNA and enhances the rate of shortening of the poly(A) tail.
Adenylate uridylate-rich elements (AUREs) are present in other cytokine mRNAs, but the SLDE is the most important element that stabilizes G-CSF mRNA in response to IL-1 or tumor necrosis factor- alpha. Additionally, there are destabilizing elements similar to SLDE found in IL-2 and IL-6. The 3'-UTR of G-CSF mRNA contains a destabilizing element that is insensitive to calcium ionophore, hence SLDE regulates G-CSF mRNA. AUDEs do not function in 5637 Bladder carcinoma cells, but the SLDE does. The two destablizing elements, SLDE and AURE, provide multiple mechanisms to regulate cytokine expression.
Neutrophils, are the most abundant type of granulocytes and are responsible for leading the first response of the immune system response against invaders. Granulocyte- |
https://en.wikipedia.org/wiki/GcvB%20RNA | The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. A deletion of GcvB RNA from Y. pestis changed colony shape as well as reducing growth. It has been shown by gene deletion that GcvB is a regulator of acid resistance in E. coli. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. A polymeric form of GcvB has recently been identified. Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of its target genes.
Targets of GcvB
GcvB has been shown to regulate a large number of genes in E. coli and Salmonella species. GcvB was shown to bind to Oppa and DppA which transport oligopeptides and dipeptides respectively. It has been shown to also regulate gltL, argT, STM, livK, livJ, brnQ, sstT and cycA which are involved in uptake of a variety of amino acids. GcvB RNA also is involved in regulating a variety of genes involved in amino acid biosynthesis such as ilvC, gdhA, thrL and serA. GcvB RNA binds PhoPQ |
https://en.wikipedia.org/wiki/GlmS%20glucosamine-6-phosphate%20activated%20ribozyme | The glucosamine-6-phosphate riboswitch ribozyme ( glmS ribozyme) is an RNA structure that resides in the 5' untranslated region (UTR) of the mRNA transcript of the glmS gene. This RNA regulates the glmS gene by responding to concentrations of a specific metabolite, glucosamine-6-phosphate (GlcN6P), in addition to catalyzing a self-cleaving chemical reaction upon activation. This cleavage leads to the degradation of the mRNA that contains the ribozyme, and lowers production of GlcN6P. The glmS gene encodes for an enzyme glutamine-fructose-6-phosphate amidotransferase, which catalyzes the formation of GlcN6P, a compound essential for cell wall biosynthesis, from fructose-6-phosphate and glutamine. Thus, when GlcN6P levels are high, the glmS ribozyme is activated and the mRNA transcript is degraded but in the absence of GlcN6P the gene continues to be translated into glutamine-fructose-6-phosphate amidotransferase and GlcN6P is produced. GlcN6P is a cofactor for this cleavage reaction, as it directly participates as an acid-base catalyst. This RNA is the first riboswitch also found to be a self-cleaving ribozyme and, like many others, was discovered using a bioinformatics approach.
Structure
The structure of the glmS ribozyme was first determined by X-ray crystallography in 2006. The tertiary structure of this RNA is characterized by three coaxial stacked helices, packed side by side. The ribozyme core contains a double pseudoknotted structure, which places the central helix |
https://en.wikipedia.org/wiki/Glycine%20riboswitch | The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. Glycine riboswitches usually consist of two metabolite-binding aptamer domains with similar structures in tandem. The aptamers were originally thought to cooperatively bind glycine to regulate the expression of downstream genes. In Bacillus subtilis, this riboswitch is found upstream of the gcvT operon which controls glycine degradation. It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation.
The originally discovered, truncated version of the glycine riboswitch exhibits sigmoidal binding curves with Hill coefficients greater than one, which led to the idea of positive cooperativity between the two aptamer domains. Data in 2012 shows that cooperative binding does not occur in the switch with its extended 5' leader, though the purpose of the switch's dual aptamers is still uncertain.
Atomic resolution structures of portions of glycine riboswitches have been obtained by X-ray crystallography.
In vivo experiments demonstrated that glycine does not need to bind both aptamers for regulation. Mutation to the first aptamer caused greatest reduction in downstream gene expression, while mutation to the second one had varying effects. Glycine-induced expression of the gcvT operon is needed for B. subtilise growth, swarming motility and biofilm formation (in high glycine environment).
References
External links
C |
https://en.wikipedia.org/wiki/Group%20I%20catalytic%20intron | Group I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions (P1-P9). These fold to essentially two domains – the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). The secondary structure mark-up for this family represents only this conserved core. Group I introns often have long open reading frames inserted in loop regions.
Catalysis
Splicing of group I introns is processed by two sequential transesterification reactions. The exogenous guanosine or guanosine nucleotide (exoG) first docks onto the active G-binding site located in P7, and its 3'-OH is aligned to attack the phosphodiester bond at the 5' splice site located in P1, resulting in a free 3'-OH group at the upstream exon and the exoG being attached to the 5' end of the intron. Then the terminal G (omega G) of the intron swaps the exoG and occupies the G-binding site to organize the second ester-transfer reaction: the 3'-OH group of the upstream exon in P1 is aligned to attack the 3' splice site in P10, leading to the ligation of the adjacent upstream and downstream exons and release of the catalytic intron.
Two-metal-ion mechanism seen in protein polymerases and phosphatases was proposed to be used by group I and group II introns to process the phosphoryl transfer reactions, which w |
https://en.wikipedia.org/wiki/Mir-103/107%20microRNA%20precursor | The miR-103 microRNA precursor (homologous to miR-107), is a short non-coding RNA gene involved in gene regulation.
miR-103 and miR-107 have now been predicted or experimentally confirmed in human.
microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In this case the mature sequence comes from
the 5' arm of the precursor. The mature products are thought to have regulatory roles through complementarity to mRNA.
mir-103 and mir-107 were noted as being upregulated in obese mice and were subsequently found to have a key role in insulin sensitivity. This led to a suggestion that these microRNAs represent potential targets for the treatment of type 2 diabetes.
mir-103 has also been linked with chronic pain and intestinal cell proliferation.
Recently, miR-103-3p was shown to target the 5' untranslated region (5' UTR) of GPRC5A's mRNA in pancreatic cancer. This is one of only a handful of known instances where a miRNA targets the 5' UTR of a mRNA.
References
External links
miRBase family MIPF0000024
MicroRNA |
https://en.wikipedia.org/wiki/Hairy%20RNA%20localisation%20element%20%28HLE%29 | The hairy localisation element (HLE) is an RNA element found in the 3' UTR of the hairy gene. HLE contains two stem-loops. HLE is essential for the mediation of apical localisation and the two stem-loop structures act to allow the recognition of hairy mRNA by the localisation machinery. HLE is found in Drosophila species.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Heat%20shock%20protein%2070%20%28Hsp70%29%20internal%20ribosome%20entry%20site%20%28IRES%29 | The heat shock protein 70 (Hsp70) internal ribosome entry site (IRES) is an RNA element that allows cap independent translation during conditions such as heat shock and stress. It has been shown that the 216 nucleotide long 5' UTR contains internal ribosome entry site activity.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Mucor%20hiemalis | Mucor hiemalis is among the zygosporic fungi found in unspoiled foods. It has different industrial importance as biotransforming agents of pharmacological and chemical compounds.
Morphology and cell structure
Mucor hiemalis grows in expanding gray colonies. It grows branched sporangiophores that yielding yellow to dark brown sporangia which can mate to form black-brown, spiny zygospores.
Physiology
Mucor hiemalis is nitrate positive and requires thiamin to grow.
References
External links
Index Fungorum
USDA ARS Fungal Database
Fungal plant pathogens and diseases
Mucoraceae
Fungi described in 1903 |
https://en.wikipedia.org/wiki/Hepatitis%20C%20stem-loop%20IV | The Hepatitis C stem-loop IV is part of a putative RNA element found in the NS5B coding region. This element along with stem-loop VII, is important (but not essential) for colony formation, though its exact function and mechanism are unknown.
See also
Hepatitis C alternative reading frame stem-loop
Hepatitis C virus (HCV) cis-acting replication element (CRE)
Hepatitis C virus 3'X element
Hepatitis E virus cis-reactive element
References
External links
Cis-regulatory RNA elements
Hepatitis C virus |
https://en.wikipedia.org/wiki/Mir-148/mir-152%20microRNA%20precursor%20family | In molecular biology, miR-148 is a microRNA whose expression has been demonstrated in human (MI0000253), mouse (MI0000550), rat (MI0000616) and zebrafish (MI0002015). miR-148 has also been predicted in chicken (MI0001189).
These predicted hairpin precursor sequence are related to those of miR-152, which has been expressed in mouse (MI0000174) and is predicted in human (MI0000462).
The hairpin precursors (represented here) are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 3' arm of the hairpin.
Targets of miR-148
MicroRNAs act by lowering the expression of genes by binding to target sites in the 3' UTR of the mRNAs. However recently it was shown by Duursma and colleagues that miR-148 down regulates Dnmt3b by binding to a region in the protein coding region.
References
External links
miRBase family page
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Hepatitis%20C%20virus%203%27X%20element | The hepatitis C virus 3′X element is an RNA element which contains three stem-loop structures that are essential for replication.
See also
Hepatitis C alternative reading frame stem-loop
Hepatitis C stem-loop IV
Hepatitis C virus stem-loop VII
Hepatitis C virus (HCV) cis-acting replication element (CRE)
References
External links
Cis-regulatory RNA elements
Hepatitis C virus |
https://en.wikipedia.org/wiki/Hepatitis%20C%20virus%20cis-acting%20replication%20element | The Hepatitis C virus (HCV) cis-acting replication element (CRE) is an RNA element which is found in the coding region of the RNA-dependent RNA polymerase NS5B. Mutations in this family have been found to cause a blockage in RNA replication and it is thought that both the primary sequence and the structure of this element are crucial for HCV RNA replication.
See also
Hepatitis C alternative reading frame stem-loop
Hepatitis C virus 3'X element
Hepatitis C virus stem-loop VII
Hepatitis C stem-loop IV
Hepatitis C
References
External links
Cis-regulatory RNA elements
Hepatitis C virus |
https://en.wikipedia.org/wiki/Hepatitis%20C%20virus%20internal%20ribosome%20entry%20site | The Hepatitis C virus internal ribosome entry site, or HCV IRES, is an RNA structure within the 5'UTR of the HCV genome that mediates cap-independent translation initiation.
Protein translation of most eukaryotic mRNAs occurs by a cap-dependent mechanism and requires association of Met-tRNAiMet, several eukaryotic initiation factors, and GTP with the 40S ribosomal subunit, recruitment to the 5' cap, and scanning along the 5' UTR to reach to start codon. In contrast, translation of hepatitis C virus (HCV) mRNA is initiated by a different mechanism from the usual 5' cap-binding model. This alternate mechanism relies on the direct binding of the 40S ribosomal subunit by the internal ribosome entry site (IRES) in the 5' UTR of HCV RNA. The HCV IRES adopts a complex structure, and may differ significantly from IRES elements identified in picornaviruses. A small number of eukaryotic mRNA have been shown to be translated by internal ribosome entry.
IRES structure
Nucleotides 1–40 of the HCV mRNA are thought not to contribute to translation, and are rather required for genomic RNA replication. The remainder of the HCV 5'-UTR consists of three domains, namely domains II-IV (domain I is located on the 5'-end of the mRNA).
Mechanism of action
HCV IRES independently binds two components of eukaryotic translation initiation machinery, the multiprotein initiation factor eIF3 and 40S small ribosomal subunit. Moreover, it binds 40S in such a manner that AUG initiator codon is positio |
https://en.wikipedia.org/wiki/Hepatitis%20C%20virus%20stem-loop%20VII | Hepatitis C virus stem-loop VII is a regulatory element found in the coding region of the RNA-dependent RNA polymerase gene, NS5B. Similarly to stem-loop IV, the stem-loop structure is important (but not essential) for colony formation, though its exact function and mechanism are unknown.
See also
Hepatitis C alternative reading frame stem-loop
Hepatitis C virus (HCV) cis-acting replication element (CRE)
Hepatitis C virus 3'X element
References
External links
Cis-regulatory RNA elements
Hepatitis C virus |
https://en.wikipedia.org/wiki/Hepatitis%20delta%20virus%20ribozyme | The hepatitis delta virus (HDV) ribozyme is a non-coding RNA found in the hepatitis delta virus that is necessary for viral replication and is the only known human virus that utilizes ribozyme activity to infect its host. The ribozyme acts to process the RNA transcripts to unit lengths in a self-cleavage reaction during replication of the hepatitis delta virus, which is thought to propagate by a double rolling circle mechanism. The ribozyme is active in vivo in the absence of any protein factors and was the fastest known naturally occurring self-cleaving RNA at the time of its discovery.
The crystal structure of this ribozyme has been solved using X-ray crystallography and shows five helical segments connected by a double pseudoknot.
In addition to the sense (genomic version), all HDV viruses also have an antigenomic version of the HDV ribozyme. This version is not the exact complementary sequence but adopts the same structure as the sense (genomic) strand. The only "significant" differences between the two are a small bulge in P4 stem and a shorter J4/2 junction. Both the genomic and antigenomic ribozymes are necessary for replication.
HDV-like ribozymes
The HDV ribozyme is structurally and biochemically related to many other self-cleaving ribozymes. These other ribozymes are often referred to as examples of HDV ribozymes, because of these similarities, even though they are not found in hepatitis delta viruses. They can also be referred to as "HDV-like" to indicate this |
https://en.wikipedia.org/wiki/Mir-192/215%20microRNA%20precursor | The miR-192 microRNA precursor (homologous to miR-215), is a short non-coding RNA
gene involved in gene regulation.
miR-192 and miR-215 have now been predicted or experimentally confirmed in mouse and human.
microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In this case the mature sequence comes from the 5' arm of the precursor. The mature products are thought to have
regulatory roles through complementarity to mRNA.
mir-192 and mir-215 are thought to be positive regulators of p53, a human tumour suppressor. They are also overexpressed in gastric cancer, and could be used as biomarkers or therapeutic targets. It has also been suggested that mir-192 could be used as a biomarker for drug-induced liver damage.
miR-215 and miR-192 are also both implicated in major depressive disorder. Small-RNA sequencing reveals upregulated expression for both miR-215 and miR-192 in the synaptosomes derived from the dorsolateral prefrontal cortex of MDD subjects.
References
External links
miRBase family MIPF0000063
MicroRNA |
https://en.wikipedia.org/wiki/Hepatitis%20E%20virus%20cis-reactive%20element | The hepatitis E virus cis-reactive element is an RNA element that is believed to be essential for "some step in gene expression". The mutation of this element resulted in hepatitis E strains which were unable to infect rhesus macaques (Macaca mulatta).
References
External links
Cis-regulatory RNA elements
Hepeviridae |
https://en.wikipedia.org/wiki/HgcC%20family%20RNA | HgcC is a small non coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein.
This ncRNA gene was originally identified by computationally searching the genome of the thermophilic archea Methanococcus jannaschii for non-coding regions of high guanine-cytosine (GC) content. The original rational for this search was based on the observation that the genomes of these bacteria are adenosine-thiamine (AT) rich and consequently have a low GC content. However, the GC content of ribosomal RNA (rRNA) and transfer RNA (tRNA) genes in hyperthermophiles shows a strong correlation with optimal growth temperature. It was proposed that non coding regions of high GC-content might encode functional RNA products. The computational screen identified a number of novel ncRNA genes in the genome of M.jannaschii. These were named hgc- ("high GC") A, B, C, D, E, F and G. Two other homologues were detected called HhcA and HhcB after "homologue of hgcC". A further RNA element, SscA RNA, was also identified.
The HgcC gene product was experimentally validated by Northern blot and RACE-PCR analysis. The function of this ncRNA is unknown.
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/HgcE%20RNA | The HgcE RNA (also known as Pf3 RNA) gene is a non-coding RNA that was identified computationally and experimentally verified in AT-rich hyperthermophiles. The genes in the screen were named hgcA through hgcG ("high GC"). The HgcE has been renamed as Pf3 and identified as an H/ACA snoRNA that is suggested to target 23S rRNA for pseudouridylation. This RNA contains two K-turn motifs. It was later identified as Pab105 H/ACA snoRNA with rRNA targets.
See also
HgcC family RNA
HgcF RNA
HgcG RNA
SscA RNA
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/HgcF%20RNA | The HgcF RNA gene is a non-coding RNA identified computationally and experimentally verified in AT-rich hyperthermophiles. The genes were named hgcA through hgcG ("high GC"). It was later identified as Pab35 H/ACA snoRNA with rRNA targets.
See also
HgcC family RNA
HgcE RNA
HgcG RNA
SscA RNA
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/Mir-46/mir-47/mir-281%20microRNA%20precursor%20family | In molecular biology, mir-46 (MI0000017) and mir-47 (MI0000018) are microRNA expressed in C. elegans from related hairpin precursor sequences. The predicted hairpin precursor sequences for Drosophila mir-281 (MI0000366, MI0000370) are also related and, hence, belong to this family. The hairpin precursors (represented here) are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequences are expressed from the 3' arms of the hairpin precursors.
References
External links
MI0000017
MI0000018
MI0000366
MI0000370
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-8/mir-141/mir-200%20microRNA%20precursor%20family | The miR-8 microRNA precursor (homologous to miR-141, miR-200, miR-236), is a short non-coding RNA
gene involved in gene regulation. miR-8 in Drosophila melanogaster is expressed from the 3' arm of related precursor hairpins (represented here), along with miR-200, miR-236, miR-429 and human and mouse homolog miR-141. Members of this precursor family have now been predicted or experimentally confirmed in a wide range of species. The bounds of the precursors are predicted based on conservation and base pairing and are not generally known.
The miR-200 family is highly conserved in bilaterian animals, with miR-8 as the sole homolog in Drosophila. This species has accordingly been used heavily in work looking to uncover the biological function of the miR-200 family. miR-8 has been observed at all developmental stages of the embryo, and is present in cultured S2 cells of D. melanogaster. Its expression has been seen to be strongly upregulated in larvae and this expression then sustained through to adulthood.
Targets of miR-8
The atrophin gene has been shown to be a target of Drosophila miR-8., with suggestion that this target is also conserved in mammalian miR-8. Elevated atrophin activity in miR-8 mutant phenotypes has been observed, this in turn inducing elevated neural apoptosis and also behavioural defects. The atrophin mRNA increase in miR-8 mutants occurs post-transcriptionally, with miR-8 binding leading to destabilisation of atrophin mRNA. miR-8 acts to control atrophin |
https://en.wikipedia.org/wiki/Mir-9/mir-79%20microRNA%20precursor%20family | The miR-9 microRNA (homologous to miR-79), is a short non-coding RNA gene involved in gene regulation. The mature ~21nt miRNAs are processed from hairpin precursor sequences by the Dicer enzyme. The dominant mature miRNA sequence is processed from the 5' arm of the mir-9 precursor, and from the 3' arm of the mir-79 precursor. The mature products are thought to have regulatory roles through complementarity to mRNA. In vertebrates, miR-9 is highly expressed in the brain, and is suggested to regulate neuronal differentiation. A number of specific targets of miR-9 have been proposed, including the transcription factor REST and its partner CoREST.
Species distribution
miR-9 has been identified in Drosophila (MI0000129), mouse (MI0000720) and human (MI0000466), and the related miR-79 in C. elegans (MI0000050) and Drosophila melanogaster (MI0000374).
Role in disease
microRNAs have been implicated in human cancer in a number of studies. It has been shown that human miR-9 expression levels are reduced in many breast cancer samples due to hypermethylation an epigenetic modification. Hildebrandt et al. show that two genes encoding for has-miR-9 are significantly hypermethylated in clear cell renal carcinoma tumours.
References
Further reading
External links
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/PrrB/RsmZ%20RNA%20family | The PrrB/RsmZ RNA family are a group of related non-coding RNA molecules found in bacteria. PrrB RNA is able to phenotypically complement gacS and gacA mutants and is itself regulated by the GacS-GacA two-component signal transduction system. Inactivation of the prrB gene in Pseudomonas fluorescens F113 resulted in a significant reduction of 2, 4-diacetylphloroglucinol (Phl) and hydrogen cyanide (HCN) production, while increased metabolite production was observed when prrB was overexpressed. The prrB gene sequence contains a number of imperfect repeats of the consensus sequence 5′-AGGA-3′, and sequence analysis predicted a complex secondary structure featuring multiple putative stem-loops with the consensus sequences predominantly positioned at the single-stranded regions at the ends of the stem-loops. This structure is similar to the CsrB and RsmB regulatory RNAs (CsrB/RsmB RNA family), suggesting this RNA also interacts with a CsrA-like protein.
Studies in Legionella pneumophila have shown that the ncRNAs RsmY and RsmZ together with the proteins LetA and CsrA are involved in a regulatory cascade. Also, it appears that these ncRNAs are regulated by RpoS sigma-factor.
See also
CsrB/RsmB RNA family
CsrC RNA family
RsmY RNA family
RsmX
RsmW sRNA
CsrA protein
References
Further reading
External links
Pfam page for the CsrA protein family
Non-coding RNA |
https://en.wikipedia.org/wiki/Pyrococcus%20C/D%20box%20small%20nucleolar%20RNA | In molecular biology, Pyrococcus C/D box small nucleolar RNA are non-coding RNA (ncRNA) molecules identified in the archaeal genus Pyrococcus which function in the modification of ribosomal RNA (rRNA) and transfer RNA (tRNA). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell, which is a major site of ribosomal RNA and snRNA biogenesis, but there is no corresponding visible structure in archaeal cells. This group of ncRNAs are known as small nucleolar RNAs (snoRNA) and also often referred to as a guide RNAs because they direct associated protein enzymes to add a modification to specific nucleotides in target RNAs. C/D box RNAs guide the addition of a methyl group (-CH3) to the 2'-O position in the RNA backbone.
Computational screens of archaeal genomes have identified C/D box snoRNAs in a number of genomes. In particular 46 small RNAs were identified to be conserved in the genomes of three hyperthermophile Pyrococcus species.
References
External links
snoRNAdb
Small nuclear RNA |
https://en.wikipedia.org/wiki/SraC/RyeA%20RNA | The SraC/RyeA RNA is a non-coding RNA that was discovered in E. coli during two large scale screens for RNAs. The function of this RNA is currently unknown. This RNA overlaps the SdsR/RyeB RNA on the opposite strand suggesting that the two RNAs may act in a concerted manner.
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/OmrA-B%20RNA | The OmrA-B RNA gene family (also known as SraE RNA, RygA and RygB and OmrA and OmrB) is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in E. coli during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding.
They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions.
Together with the RNA chaperone Hfq, OmrA-B positively controls bacterial motility and negatively controls the production of acidic exopolysaccharide amylovoran in plant pathogen Erwinia amylovora.
References
External links
EcoGene entry for OmrA and OmrB
EcoliWiki entry for OmrA and OmrB
Non-coding RNA |
https://en.wikipedia.org/wiki/Snake%20H/ACA%20box%20small%20nucleolar%20RNA | In molecular biology, Snake H/ACA box small nucleolar RNA refers to a number of very closely related non-coding RNA (ncRNA) genes identified in snakes which have been predicted to be small nucleolar RNAs (snoRNAs). This type of ncRNA is involved in the biogenesis of other small nuclear RNAs and are often referred to as 'guide' RNAs. They are usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis.
These snoRNA genes were initially identified in the introns of the cardiotoxin 4 and cobrotoxin genes of the Taiwan cobra (Bungarus multicinctus) and the Taiwan banded krait (Bungarus multicinctus) during sequencing of these genes. These snoRNAs are predicted to act as H/ACA box type methylation guides as they have the predicted hairpin-hinge-hairpin-tail structure and extended regions of complementarity to 5S ribosomal RNA (rRNA).
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Infectious%20bronchitis%20virus%20D-RNA | The Infectious bronchitis virus D-RNA is an RNA element known as defective RNA or D-RNA. This element is thought to be essential for viral replication and efficient packaging of avian infectious bronchitis virus (IBV) particles.
Coronavirus D-RNA like that of IBV, are produced during high multiplicity of infection and contain cis-acting sequences which are required for viral replication. While it is unclear exactly how IBV D-RNA is made, it is thought to be synthesized in a similar manner as subgenomic mRNA (sg mRNA), with most of the genomic sequence left out of the product. Additionally, sg mRNA can also be synthesized from the IBV D-RNA, although the mechanism of that process is still largely unknown.
IBV D-RNA is often used in the reverse genetics approach to experimentally induce heterologous gene expression and site-specific mutagenesis of the coronavirus genome. However, a translation associated sequence (TAS), which is normally used to transcribe sg mRNA and is derived from gene 5 of the Beaudette strain of IBV, is needed as a promoter to regulate heterologous gene expression. It is also thought that TAS may program some IBV D-RNA to synthesize sg mRNA, which are necessary for homologous gene protein synthesis. In particular, IBV D-RNA CD-61 is used to experimentally produce recombinant IBV vaccines. D-RNA CD-61 was created from the naturally occurring IBV D-RNA CD-91, which is produced by multiple passage of high concentration IBV in chick kidney (CK) cells. The IB |
https://en.wikipedia.org/wiki/Insertion%20sequence%20IS1222%20ribosomal%20frameshifting%20element | The Insertion sequence IS1222 ribosomal frameshifting element is an RNA element found in the insertion sequence IS222. The ribosomal frameshifting element stimulates frameshifting which is known to be required for transposition.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Insulin-like%20growth%20factor%20II%20IRES | The insulin-like growth factor II (IGF-II) internal ribosome entry site IRES is found in the 5' UTR of IGF-II leader 2 mRNA. This RNA element allows cap-independent translation of the mRNA and it is thought that this family may facilitate a continuous IGF-II production in rapidly dividing cells during development. Ribosomal scanning on human insulin-like growth factor II (IGF-II) is hard to comprehend due to one open reading frame and the ability for the hormone to fold into a stable structure.
References
External links
IRESite page for IGF2 leader2
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Interferon%20gamma%205%27%20UTR%20regulatory%20element | Interferon gamma 5' UTR regulatory elements are a family of regulatory RNAs. This family represents a pseudoknot containing stem-loop structure found in the 5' UTR of interferon-gamma mRNA. This structure is thought to be involved in translational regulation and the pseudoknot has been found to activate protein kinase R (PKR) which is known to be a translational inhibitor. Mutations in the pseudoknot structure have been found to reduce PKR activation and increase the translation of interferon-gamma.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Iron%20response%20element | In molecular biology, the iron response element or iron-responsive element (IRE) is a short conserved stem-loop which is bound by iron response proteins (IRPs, also named IRE-BP or IRBP). The IRE is found in UTRs (untranslated regions) of various mRNAs whose products are involved in iron metabolism. For example, the mRNA of ferritin (an iron storage protein) contains one IRE in its 5' UTR. When iron concentration is low, IRPs bind the IRE in the ferritin mRNA and cause reduced translation rates. In contrast, binding to multiple IREs in the 3' UTR of the transferrin receptor (involved in iron acquisition) leads to increased mRNA stability.
Mechanism of action
The two leading theories describe how iron probably interacts to impact posttranslational control of transcription. The classical theory suggests that IRPs, in the absence of iron, bind avidly to the mRNA IRE. When iron is present, it interacts with the protein to cause it to release the mRNA. For example, In high iron conditions in humans, IRP1 binds with an iron-sulphur complex [4Fe-4S] and adopts an aconitase conformation unsuitable for IRE binding. In contrast, IRP2 is degraded in high iron conditions. There is variation in affinity between different IREs and different IRPs.
In the second theory two proteins compete for the IRE binding site—both IRP and eukaryotic Initiation Factor 4F (eIF4F). In the absence of iron IRP binds about 10 times more avidly than the initiation factor. However, when Iron interacts at |
https://en.wikipedia.org/wiki/IS061%20RNA | The ISO61 (IsrA) RNA is a bacterial non-coding RNA that is found between the abgR and ydaL genes in Escherichia coli and Shigella flexneri. It was discovered using a computational screen of the E. coli genome. Subsequent characterisation of ISO61 region has revealed that the reverse strand is actually a CsrA binding ncRNA called McaS and that it has a role in biofilm formation control. Furthermore, it has been shown that McaS(IsrA) exists as ribonucleoprotein particles (sRNPs), which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and PNPase.
See also
IS102 RNA
IS128 RNA
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/IS102%20RNA | The IS102 RNA is a non-coding RNA that is found in bacteria such as Shigella flexneri and Escherichia coli. The RNA is 208 nucleotides in length and found between the yeeP and flu genes. This RNA was identified in a computational screen of E. coli. The function of this RNA is unknown.
See also
IS061 RNA
IS128 RNA
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/Tymovirus/pomovirus%20tRNA-like%203%27%20UTR%20element | The tymoviruses/pomovirusesfamily tRNA-like 3' UTR element is an RNA element found in the 3' UTR of some viruses. This element acts in conjunction with UPSK RNA and a 5'-cap to enhance translation. The secondary structure of this RNA element is a cloverleaf that resembles tRNA.
References
External links
Cis-regulatory RNA elements
Tymoviridae |
https://en.wikipedia.org/wiki/IS128%20RNA | The IS128 RNA is a non-coding RNA found in bacteria such as Escherichia coli and Shigella flexneri. The RNA is 209 nucleotides in length. It is found between the sseA and sseB genes. The IS128 RNA was initially identified in a computational screen of the E. coli genome. The function of this RNA is unknown.
See also
IS061 RNA
IS102 RNA
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/Leucine%20operon%20leader | The Leucine operon leader is an RNA element found upstream of the first gene in the Leucine biosynthetic operon. The leader sequence can assume two different secondary structures known as the terminator and the anti-terminator structure. The leader also codes for very short peptide sequence that is rich in leucine amino acid. The terminator structure is recognised as a termination signal for RNA polymerase and the operon is not transcribed. This structure forms when the cell has an excess of leucine and ribosome movement over the leader transcript is not impeded. When there is a deficiency of the charged leucyl tRNA the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon. At least 6 amino acid operons are known to be regulated by attenuation.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/L-myc%20internal%20ribosome%20entry%20site%20%28IRES%29 | The L-myc internal ribosome entry site (IRES) is an RNA element present in the 5' UTR of the mRNA of L-myc that allows cap-independent translation. L-myc undergoes translation via the internal ribosome entry site and bypasses the typical eukaryotic cap-dependent translation pathway [1]. The myc family of genes when expressed are known to be involved in the control of cell growth, differentiation and apoptosis.
References
Further reading
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Luteovirus%20cap-independent%20translation%20element | The Barley yellow dwarf virus-like cap-independent translation element (BTE) is an RNA element found in the 3' UTR of some luteoviruses. This element mediates translation of genomic RNA and subgenomic RNA1 (sgRNA1).
BTEs have a consensus sequence, GGAUCCUGGGAAACAGG, embedded in series of three to six stem-loops that radiate from a central hub.
BTE has been found to bind to eIF4G and weakly to eIF4E (proteins involved in translation initiation). BTE allows translation initiation of an mRNA without a 7mG cap (required for translation in most eukaryotic mRNA). Other forms of cap-independent translation elements (CITE) exist (primarily in plant viruses from the Luteovirus, Necrovirus, Dianthovirus and Umbravirus genera of plantviruses, but also in some host mRNA; notably many heat shock mRNA lack a 7mG cap but are still translated). The general purpose of BTE and these other CITE's is to get the ribosome to begin translation without the 7mG cap. In the case of BTE it "tricks" eIF4F (eIF4E, eIF4G are parts of eIF4F) into "telling" the ribosome that a 7mG cap is present.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/YdaO/yuaA%20leader | The YdaO/YuaA leader (now called the cyclic di-AMP riboswitch) is a conserved RNA structure found upstream of the ydaO and yuaA genes in Bacillus subtilis and related genes in other bacteria. Its secondary structure and gene associations were predicted by bioinformatics.
These RNAs function as riboswitches, and sense the signaling molecule cyclic di-AMP. The interaction between the riboswitch and c-di-AMP has been revealed in atomic-resolution structures.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Lysine%20riboswitch | The Lysine riboswitch is a metabolite binding RNA element found within certain messenger RNAs that serve as a precision sensor for the amino acid lysine. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression. Lysine riboswitch are most abundant in Bacillota and Gammaproteobacteria where they are found upstream of a number of genes involved in lysine biosynthesis, transport and catabolism. The lysine riboswitch has also been identified independently and called the L box.
The lysine riboswitch controls metabolic pathways of lysine biosynthesis. In particular the metabolic flux of the tricarboxylic acid (TCA) cycle is effectively controlled by the riboswitch. Controlling metabolic flux is imperative for the development of microorganisms in cell growth, and the use of the lysine riboswitch in its applicable bacterium allows for the use of more effective strategies to accomplish control. It is more effective in comparison to various expensive and difficult methods such as utilizing a gene knockout. With lysine as an intracellular signal, the riboswitch regulates gene expression in response to specific metabolites. The lysine riboswitch was first investigated in Bacilus subtilis, located at the 5’UTR of the lysC gene coding for aspartkinase. It has since been found in E.coli (ECRS) with the ability to inhibit translation of apsrtkinase III in E.coli and accelerate mRNA decay. In both E.Coli and Bacilus subtilis, |
https://en.wikipedia.org/wiki/MicC%20RNA |
The MicC non-coding RNA (previously known as IS063 ) is located between the ompN and ydbK genes in E. coli. This Hfq-associated RNA is thought to be a regulator of the expression level of the OmpC porin protein, with a 5′ region of 22 nucleotides potentially forming an antisense interaction with the ompC mRNA. Along with MicF RNA this family may act in conjunction with EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in response to a variety of environmental stimuli. The expression of micC was shown to be increased in the presence of beta-lactam antibiotics.
See also
Two-component regulatory system
References
Further reading
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/MicF%20RNA | The micF RNA is a non-coding RNA stress response gene found in Escherichia coli and related bacteria that post-transcriptionally controls expression of the outer membrane porin gene ompF. The micF gene encodes a non-translated 93 nucleotide antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. In addition, other factors, such as the RNA chaperone protein StpA also play a role in this regulatory system. The expression of micF is controlled by both environmental and internal stress factors. Four transcriptional regulators are known to bind the micF promoter region and activate micF expression.
Species distribution
Homologues of MicF RNA have been characterised by Southern blotting in a variety of bacteria including Salmonella typhimurium, Klebsiella pneumoniae, and Pseudomonas aeruginosa. MicF has also been identified computationally in Yersinia pestis and Yersinia enterocolitica.
References
External links
Antisense RNA |
https://en.wikipedia.org/wiki/Mir-101%20microRNA%20precursor%20family | miR-101 microRNA precursor is a small non-coding RNA that regulates gene expression. Expression of miR-101 has been validated in both human (MI0000103, MI0000739) and mouse (MI0000148). This microRNA appears to be specific to the vertebrates and has now been predicted or confirmed in a wide range of vertebrate species (MIPF0000046). The precursor microRNA is a stem-loop structure of about 70 nucleotides in length that is processed by the Dicer enzyme to form the 21-24 nucleotide mature microRNA. In this case the mature sequence is excised from the 3' arm of the hairpin.
Survival analysis shows that hsa-miR-101 is associated with survival in multiple breast cancer datasets.
References
Further reading
External links
miRBase family MIPF0000046
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-10%20microRNA%20precursor%20family | The mir-10 microRNA precursor is a short non-coding RNA gene involved in gene regulation. It is part of an RNA gene family which contains mir-10, mir-51, mir-57, mir-99 and mir-100. mir-10, mir-99 and mir-100 have now been predicted or experimentally confirmed in a wide range of species. (MIPF0000033, MIPF0000025) miR-51 and miR-57 have currently only been identified in the nematode Caenorhabditis elegans (MIPF0000268, MIPF0000271).
MicroRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In this case the mature sequence comes from the 5' arm of the precursor. The mature products are thought to have regulatory roles through complementarity to mRNA.
Species distribution
The presence of miR-10 has been detected in a diverse range of bilaterian animals. It is one of the most widely distributed microRNAs in animals, it has been identified in numerous species including human, dog, cat, horse, cow, guinea pig, mouse, rat, common marmoset (Callithrix jacchus), common chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), Sumatran orangutan (Pongo abelii), northern greater galago (Otolemur garnettii), gray short-tailed opossum (Monodelphis domestica), northern treeshrew (Tupaia belangeri), European rabbit (Oryctolagus cuniculus), African bush elephant (Loxodonta africana), nine-banded armadillo (Dasypus novemcinctus), European hedgehog (Erinaceus europaeus), lesser hedgehog tenrec (Echinops t |
https://en.wikipedia.org/wiki/Mir-124%20microRNA%20precursor%20family | The miR-124 microRNA precursor is a small non-coding RNA molecule that has been identified in flies (MI0000373), nematode worms (MI0000302), mouse (MI0000150) and human (MI0000443). The mature ~21 nucleotide microRNAs are processed from hairpin precursor sequences by the Dicer enzyme, and in this case originates from the 3' arm. miR-124 has been found to be the most abundant microRNA expressed in neuronal cells. Experiments to alter expression of miR-124 in neural cells did not appear to affect differentiation. However these results are controversial since other reports have described a role for miR-124 during neuronal differentiation.
Targets of miR-124
Visvanathan et al. showed that miR-124 targets the mRNA of the anti-neural function protein SCP1 (small C-terminal domain phosphatase 1).
Makeyev et al. showed that miR-124 directly targets PTBP1 (PTB/hnRNP I) mRNA, which encodes a global repressor of alternative pre-mRNA splicing in non-neuronal cells.
Arrant et al. wrote that miR-124 changes glutamate receptor composition in the prefrontal cortex and can decrease social dysfunction in frontotemporal dementia.
Clinical medicine
Presence of the G allele, compared to the C allele, in SNP rs531564 in pri-miR-124-1, measured by PCR-RFLP in leukocyte DNA, is linked to a reduced risk of gastric cancer (e.g. GG v CC OR 0.34 95% CI 0.19-0.59, p<0.001).
References
External links
miRBase family for miR-124
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20296A/B | In molecular biology, snoRNAs HBII-296A and B belong to the C/D family of snoRNAs.
They are close paralogues sharing the same host gene (FLJ10534) and are predicted to guide 2'O-ribose methylation of the large 28S rRNA at position G4588.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-129%20microRNA%20precursor%20family | The miR-129 microRNA precursor is a small non-coding RNA molecule that regulates gene expression. This microRNA was first experimentally characterised in mouse and homologues have since been discovered in several other species, such as humans, rats and zebrafish. The mature sequence is excised by the Dicer enzyme from the 5' arm of the hairpin. It was elucidated by Calin et al. that miR-129-1 is located in a fragile site region of the human genome near a specific site, FRA7H in chromosome 7q32, which is a site commonly deleted in many cancers. miR-129-2 is located in 11p11.2.
Expression Patterns
miR-129 seems to have a tissue specific expression pattern localised to the brain in normal humans. This finding was identified initially by microarray experimentation with mouse tissue (and more specifically to the cerebellum) which was subsequently validated by the expression profiling in human tissue. However, expression in normal brain tissue was found to be relatively low and different profiling experimentation methodologies produced differing results. These differences and the low levels of detection may be attributed to the size and complexity of the human brain and the fact that specific regions of the brain were not individually tested.
Targets of miR-129
Cdk6
As with many other microRNAs, the expression profile of miR-129 changes with the onset of cancer. In many different tumour cell lines, such as gastric cancer, medulloblastoma and endometrial cancer, lung andeocarcino |
https://en.wikipedia.org/wiki/Mir-130%20microRNA%20precursor%20family | In molecular biology, miR-130 microRNA precursor is a small non-coding RNA that regulates gene expression. This microRNA has been identified in mouse (MI0000156, MI0000408), and in human (MI0000448, MI0000748). miR-130 appears to be vertebrate-specific miRNA and has now been predicted or experimentally confirmed in a range of vertebrate species (MIPF0000034). Mature microRNAs are processed from the precursor stem-loop by the Dicer enzyme. In this case, the mature sequence is excised from the 3' arm of the hairpin. It has been found that miR-130 is upregulated in a type of cancer called hepatocellular carcinoma. It has been shown that miR-130a is expressed in the hematopoietic stem/progenitor cell compartment but not in mature blood cells.
References
External links
miRBase family MIPF0000034
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-133%20microRNA%20precursor%20family | mir-133 is a type of non-coding RNA called a microRNA that was first experimentally characterised in mice. Homologues have since been discovered in several other species including invertebrates such as the fruitfly Drosophila melanogaster. Each species often encodes multiple microRNAs with identical or similar mature sequence. For example, in the human genome there are three known miR-133 genes: miR-133a-1, miR-133a-2 and miR-133b found on chromosomes 18, 20 and 6 respectively. The mature sequence is excised from the 3' arm of the hairpin. miR-133 is expressed in muscle tissue and appears to repress the expression of non-muscle genes.
Regulation
It is proposed that Insulin activates the translocation of SREBP-1c (BHLH) active form from the endoplasmic reticulum (ER) to the nucleus and, concomitantly, induces SREPB-1c expression via PI3K signaling pathway. SREBP-1c mediates MEF2C downregulation through a mechanism that remains to be determined. As a consequence of lower MEF2C binding on their enhancer region, the transcription of miR-1 and miR-133a is reduced, leading to decreased levels of their mature forms in muscle, after insulin treatment. Altered activation of PI3K and SREBP-1c may explain the defective regulation of miR-1 and miR-133a expression in response to insulin in muscle of type 2 diabetic patients.
Targets of miR-133
microRNAs act by lowering the expression of genes by binding to target sites in the 3' UTR of the mRNAs. Luo et al.. demonstrated that the H |
https://en.wikipedia.org/wiki/Mir-135%20microRNA%20precursor%20family | The miR-135 microRNA precursor is a small non-coding RNA that is involved in regulating gene expression. It has been shown to be expressed in human, mouse and rat. miR-135 has now been predicted or experimentally confirmed in a wide range of vertebrate species (MIPF0000028). Precursor microRNAs are ~70 nucleotides in length and are processed by the Dicer enzyme to produce the shorter 21-24 nucleotide mature sequence. In this case the mature sequence is excised from the 5' arm of the hairpin.
Targets of miR-135
Nagel et al.. showed that miR-135a and b target the 3' untranslated region of the APC gene.
References
External links
MIPF0000028
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-156%20microRNA%20precursor | MicroRNA (miRNA) precursor miR156 is a family of plant non-coding RNA. This microRNA has now been predicted or experimentally confirmed in a range of plant species (MIPF0000008). Animal miRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. miR156 functions in the induction of flowering by suppressing the transcripts of SQUAMOSA-PROMOTER BINDING LIKE (SPL) transcription factors gene family. It was suggested that the loading into ARGONAUTE1 and ARGONAUTE5 is required for miR156 functionality in Arabidopsis thaliana. In plants the precursor sequences may be longer, and the carpel factory (caf) enzyme appears to be involved in processing. In this case the mature sequence comes from the 5' arm of the precursor, and both Arabidopsis thaliana and rice genomes contain a number of related miRNA precursors which give rise to almost identical mature sequences. The extents of the hairpin precursors are not generally known and are estimated based on hairpin prediction. The products are thought to have regulatory roles through complementarity to mRNA.
This miRNA is involved in control of reproductive structures in liverworts.
References
Further reading
External links
MIPF0000008
MicroRNA |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20F1/F2/snoR5a | In molecular biology, Small nucleolar RNA F1/F2/snoR5a refers to a group of related non-coding RNA (ncRNA) molecules which function in the biogenesis of other small nuclear RNAs (snRNAs). These small nucleolar RNAs (snoRNAs) are modifying RNAs and usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis.
These three snoRNas identified in rice (Oryza sativa), called F1, F2 and snoR5a, belong to the H/ACA box class of snoRNAs as they have the predicted hairpin-hinge-hairpin-tail structure and has the conserved H/ACA-box motifs. The majority of H/ACA box class of snoRNAs are involved in guiding the modification of uridine) to pseudouridine in other RNAs
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-15%20microRNA%20precursor%20family | The miR-15 microRNA precursor family is made up of small non-coding RNA genes that regulate gene expression. The family includes the related mir-15a and mir-15b sequences, as well as miR-16-1, miR-16-2, miR-195 and miR-497. These six highly conserved miRNAs are clustered on three separate chromosomes. In humans miR-15a and miR-16 are clustered within 0.5 kilobases at chromosome position 13q14. This region has been found to be the most commonly affected in chronic lymphocytic leukaemia (CLL), with deletions of the entire region in more than half of cases. Both miR-15a and miR-16 are thus frequently deleted or down-regulated in CLL samples with 13q14 deletions; occurring in more than two thirds of CLL cases. The expression of miR-15a is associated with survival in triple negative breast cancer.
miR-15a/16-1 deletion has been shown to accelerate the proliferation of both human and mouse B-cells through modulation of the expression of genes controlling cell cycle progression. Studies have found the miR-15a/16-1 microRNA cluster to function as a tumour suppressor, with the oncogene BCL2 as its target. Specifically, miR-15a/16-1 downregulates BCL2 expression and is itself deleted or downregulated in tumour cells. There is a marked increase in BCL2 levels observed in advanced prostate tumour cases, which is inversely correlated with miR-15a/16-1 expression (and so corresponds to a decrease in miR-15a/16-1 levels). Inhibition of cell proliferation by the miR-15a/16-1 cluster occurs |
https://en.wikipedia.org/wiki/Mir-160%20microRNA%20precursor%20family | In molecular biology, mir-160 is a microRNA that has been predicted or experimentally confirmed in a range of plant species including Arabidopsis thaliana (mouse-ear cress) and Oryza sativa (rice). miR-160 is predicted to bind complementary sites in the untranslated regions of auxin response factor genes to regulate their expression. The hairpin precursors (represented here) are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 5' arm of the hairpin.
Specifically, 3 of A. thaliana's 23 auxin-response factor genes are thought to be post-transcriptionally regulated by mir-160. When one of these targets (ARF17) is manipulated to become miRNA-resistant, several developmental defects can be observed in the host plant. This experiment has been repeated with another mir-160 target, ARF10, and results highlighted a regulatory role in post-embryonic development and seed germination.
References
External links
MIPF0000032
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-166%20microRNA%20precursor | The plant mir-166 microRNA precursor is a small non-coding RNA gene. This microRNA (miRNA) has now been predicted or experimentally confirmed in a wide range of plant species. microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In this case the mature sequence comes from the 3' arm of the precursor, and both Arabidopsis thaliana and rice genomes contain a number of related miRNA precursors which give rise to almost identical mature sequences. The mature products are thought to have regulatory roles through complementarity to messenger RNA.
References
External links
MIPF0000004
MicroRNA |
https://en.wikipedia.org/wiki/Mir-16%20microRNA%20precursor%20family | The miR-16 microRNA precursor family is a group of related small non-coding RNA genes that regulates gene expression. miR-16, miR-15, mir-195 and miR-497 are related microRNA precursor sequences from the mir-15 gene family (). This microRNA family appears to be vertebrate specific and its members have been predicted or experimentally validated in a wide range of vertebrate species (MIPF0000006).
Background
The human miR-16 precursor was discovered through detailed expression profile and Karyotype analyses of patients by Calin and colleagues. Karyotyping of chromosome structures from individuals with B-cell chronic lymphocytic leukaemias (B-CLL) found that more than half have alterations in the 13q14 region. Deletions of this well characterised 1 megabase region of the genome was also observed in approximately 50% of mantle cell lymphoma, up to 40% of multiple myeloma, and 60% of prostate cancers. Comprehensive screenings of the region at the time did not provide consistent evidence of involvement from any of the known genes at the time. Using CD5+ B-lymphocytes, which is known to accumulate with B-CLL progression, the minimal region lost from 13q14 region was scrutinised for regulatory elements. Publicly available sequence databases were used to identify a gene cluster which encodes the homologue to the human miR15 and miR16 from the Caenorhabditis elegans.
Gene targets
In the original publication which identified the action of miR15 and miR16 in the development of B-CLL, |
https://en.wikipedia.org/wiki/Mir-172%20microRNA%20precursor%20family | The mir-172 microRNA is thought to target mRNAs coding for APETALA2-like transcription factors. It has been verified experimentally in the model plant, Arabidopsis thaliana (mouse-ear cress). The mature sequence is excised from the 3' arm of the hairpin.
References
Further reading
External links
MI0000215
MI0001139
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-17%20microRNA%20precursor%20family | The miR-17 microRNA precursor family are a group of related small non-coding RNA genes called microRNAs that regulate gene expression. The microRNA precursor miR-17 family, includes miR-20a/b, miR-93, and miR-106a/b. With the exception of miR-93, these microRNAs are produced from several microRNA gene clusters, which apparently arose from a series of ancient evolutionary genetic duplication events, and also include members of the miR-19, and miR-25 families. These clusters are transcribed as long non-coding RNA transcripts that are processed to form ~70 nucleotide microRNA precursors, that are subsequently processed by the Dicer enzyme to give a ~22 nucleotide products. The mature microRNA products are thought to regulate expression levels of other genes through complementarity to the 3' UTR of specific target messenger RNA.
The paralogous miRNA gene clusters that give rise to miR-17 family microRNAs (miR-17~92, miR-106a~363, and miR-106b~25) have been implicated in a wide variety of malignancies and are sometimes referred to as oncomirs. The oncogenic potential of these non-protein encoding genes was first identified in mouse viral tumorigenesis screens.
In humans, the activating mutations of miR-17~92 have been identified in non-Hodgkin's lymphoma, whereas the miRNA constituents of the clusters are overexpressed in a multiple cancer types. High level expression of miR-17 family members induces cell proliferation, whereas deletion of the miR-17~92 cluster, in mice, is let |
https://en.wikipedia.org/wiki/Mir-181%20microRNA%20precursor | In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. MicroRNAs (miRNAs) are transcribed as ~70 nucleotide precursors and subsequently processed by the RNase-III type enzyme Dicer to give a ~22 nucleotide mature product. In this case the mature sequence comes from the 5' arm of the precursor. They target and modulate protein expression by inhibiting translation and / or inducing degradation of target messenger RNAs. This new class of genes has recently been shown to play a central role in malignant transformation. miRNA are downregulated in many tumors and thus appear to function as tumor suppressor genes. The mature products miR-181a, miR-181b, miR-181c or miR-181d are thought to have regulatory roles at posttranscriptional level, through complementarity to target mRNAs. miR-181 which has been predicted or experimentally confirmed in a wide number of vertebrate species as rat, zebrafish, and in the pufferfish (see below) (MIPF0000007).
Expression
It has been shown that miR-181 is preferentially expressed in the B-lymphoid cells of mouse bone marrow, but also in the retina and brain. In humans, this microRNA is involved in the mechanisms of immunity, and in many different cancers (see below) it was found to be expressed at a particularly low level.
Genome location
Human
miR-181a1 and miR-181b1 are clustered together and located on the chromosome 1 (37.p5), miR-181a2 and miR-181b2 are clustered together and located on the chromosome 9 (37.p5). |
https://en.wikipedia.org/wiki/Mir-194%20microRNA%20precursor%20family | In molecular biology, miR-194 microRNA precursor is a small non-coding RNA gene that regulated gene expression. Its expression has been verified in mouse (MI0000236, MI0000733) and in human (MI0000488, MI0000732). mir-194 appears to be a vertebrate-specific miRNA and has now been predicted or experimentally confirmed in a range of vertebrate species (MIPF0000055). The mature microRNA is processed from the longer hairpin precursor by the Dicer enzyme. In this case, the mature sequence is excised from the 5' arm of the hairpin.
See also
MIR194-1
References
External links
miRBase family MIPF0000055
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-196%20microRNA%20precursor%20family | miR-196 is a non-coding RNA called a microRNA that has been shown to be expressed in humans (MI0000238, MI0000279) and mice (MI0000552, MI0000553).
miR-196 appears to be a vertebrate specific microRNA and has now been predicted or experimentally confirmed in a wide range of vertebrate species (MIPF0000031). In many species the miRNA appears to be expressed from intergenic regions in HOX gene clusters. The hairpin precursors are predicted based on base pairing and cross-species conservation—their extents are not known. In this case the mature sequence is excised from the 5' arm of the hairpin.
It has been suggested that a rare SNP (rs11614913) that overlaps hsa-mir-196a-2 has been found to be associated with non-small cell lung carcinoma.
Further reading
References
External links
MIPF0000031
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-199%20microRNA%20precursor | The miR-199 microRNA precursor is a short non-coding RNA
gene involved in gene regulation.
miR-199 genes have now been predicted or experimentally confirmed in mouse, human and a further 21 other species. microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. The mature products are thought to have regulatory roles through complementarity to mRNA.
Origin and evolution of miR-199
miR-199 has been shown to be a vertebrate specific miR family that emerge at the origin of the vertebrate lineage Three paralogs of miR-199 can usually be found in non-teleost vertebrate species and 4 to 5 copies in the teleost species. All miR-199 genes are located on opposite strand of orthologous intron of Dynamin genes. Within Dynamin3 gene (Dnm3), miR-199 is associated with miR-214 and both miRs are transcribed together as a common primary transcript, demonstrated in mouse, human and zebrafish.
Targets and expression of miR-199
miR-199 has been shown to be implicated in a wide variety of cellular and developmental mechanisms such as various cancer development and progression, cardiomyocytes protection or skeletal formation.
Using microarray and immunoblotting analyses it has been shown that miR-199a* targets the Met proto-oncogene.
MicroRNA hsa-miR-199a is a regulator of IκB kinase-β (IKKβ) expression.
Using TaqMan real-time quantitative PCR array methods, miRNA expression has been profiled. miR-199a, one of t |
https://en.wikipedia.org/wiki/Mir-19%20microRNA%20precursor%20family | There are 89 known sequences today in the microRNA 19 (miR-19) family but it will change quickly. They are found in a large number of vertebrate species. The miR-19 microRNA precursor is a small non-coding RNA molecule that regulates gene expression. Within the human and mouse genome there are three copies of this microRNA that are processed from multiple predicted precursor hairpins:
mouse:
* miR-19a on chromosome 14 (MI0000688)
* miR-19b-1 on chromosome 14 (MI0000718)
* miR-19b-2 on chromosome X (MI0000546)
human:
* miR-19a on chromosome 13 (MI0000073)
* miR-19b-1 on chromosome 13 (MI0000074)
* miR-19b-2 on chromosome X (MI000075).
MiR-19 has now been predicted or experimentally confirmed (MIPF0000011). In this case the mature sequence is excised from the 3' arm of the hairpin precursor.
Origins
MicroRNA are ubiquitous in higher eukaryotes, and show varying patterns of expression in specific cell types. MiR-19 has been identified in a diverse range of vertebrate animals including green anole (Anolis carolinensis), primates (gorilla, human, ...), cattle (Bos taurus), dog (Canis familiaris), Chinese hamster (Cricetulus griseus), zebrafish (Danio rerio), horse (Equus caballus), Takifugu rubripes, Tetraodon nigroviridis, chicken (Gallus gallus), gray short-tailed opossum (Monodelphis domestica), platypus (Ornithorhynchus anatinus), Japanese medaka (Oryzias latipes), African clawed frog (Xenopus laevis), Tasmanian devil (Sarcophilus harrisii), pig (Sus scrofa) and z |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20psi18S-841/snoR66 | In molecular biology, the psi18S-841 is a member of the H/ACA class of snoRNA. This family is responsible for guiding the modification of uridine 841 in Drosophila 18S rRNA to pseudouridine.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-1%20microRNA%20precursor%20family | The miR-1 microRNA precursor is a small micro RNA that regulates its target protein's expression in the cell. microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give products at ~22 nucleotides. In this case the mature sequence comes from the 3' arm of the precursor. The mature products are thought to have regulatory roles through complementarity to mRNA. In humans there are two distinct microRNAs that share an identical mature sequence, and these are called miR-1-1 and miR-1-2.
These micro RNAs have pivotal roles in development and physiology of muscle tissues including the heart. MiR-1 is known to play an important role in heart diseases such as hypertrophy, myocardial infarction, and arrhythmias. Studies have shown that MiR-1 is an important regulator of heart adaption after ischemia or ischaemic stress and it is upregulated in the remote myocardium of patients with myocardial infarction. Also MiR-1 is downregulated in myocardial infarcted tissue compared to healthy heart tissue. Plasma levels of MiR-1 can be used as a sensitive biomarker for myocardial infarction.
Targets of miR-1
The heat shock protein, HSP60 is also known to be a target for post-transcriptional regulation by miR-1 and miR-206. HSP60 is a component of the defence mechanism against diabetic myocardial injury and its level is reduced in the diabetic myocardium. In both in vivo and in vitro experiments increased levels of glucose in myocardiomyctes l |
https://en.wikipedia.org/wiki/MiR-218%20microRNA%20precursor%20family | miR-218 microRNA precursor is a small non-coding RNA that regulates gene expression by antisense binding.
miR-218 appears to be a vertebrate specific microRNA and has now been predicted and experimentally confirmed in a wide range of vertebrate species. The extents of the hairpin precursors are not known. In this case the mature sequence in excised from the 5'arm of the hairpin.
miR-218 is specifically expressed by mammalian motor neurons during embryonic development into adulthood, and motor neurons lacking expression of miR-218 exhibit hyperexcitability, neuromuscular junction failure, and neurodegeneration, as demonstrated by knockout mouse models.
The involvement of miR-218 in cancer has also been investigated. miR-218, along with miR-585, has been found to be silenced by DNA methylation in oral squamous cell carcinoma. It is also downregulated in Nasopharyngeal carcinoma, with artificially-induced expression serving to slow tumour growth. miR-218 has also been found to have tumour suppressing qualities in bladder cancer cells. miR-218 expression was associated with overall survival in breast cancer datasets.
References
External links
MicroRNA |
https://en.wikipedia.org/wiki/Mir-219%20microRNA%20precursor%20family | In molecular biology, the microRNA miR-219 was predicted in vertebrates by conservation between human, mouse and pufferfish and cloned in pufferfish. It was later predicted and confirmed experimentally in Drosophila. Homologs of miR-219 have since been predicted or experimentally confirmed in a wide range of species, including the platyhelminth Schmidtea mediterranea, several arthropod species and a wide range of vertebrates (MIPF0000044). The hairpin precursors (represented here) are predicted based on base pairing and cross-species conservation; their extents are not known. In this case, the mature sequence is excised from the 5' arm of the hairpin.
miR-219 has also been linked with NMDA receptor signalling in humans by targeting CaMKIIγ (a kind of protein kinase dependent to calcium and calmodulin) expression. And it has been suggested that deregulation of this miRNA can lead to the expression of mental disorders such as schizophrenia. Recent findings show that miR-219 is linked with Tau toxicity, suggesting that miR-219 is involved in neurodegenerative disease, such as Alzheimer's disease, Parkinson's disease etc.
References
External links
MIPF0000044
MicroRNA of the month at the miRNA blog
MicroRNA |
https://en.wikipedia.org/wiki/Mir-24%20microRNA%20precursor%20family | The miR-24 microRNA precursor is a small non-coding RNA molecule that regulates gene expression. microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a mature ~22 nucleotide product. In this case the mature sequence comes from the 3' arm of the precursor. The mature products are thought to have regulatory roles through complementarity to mRNA. miR-24 is conserved in various species, and is clustered with miR-23 and miR-27, on human chromosome 9 and 19. Recently, miR-24 has been shown to suppress expression of two crucial cell cycle control genes, E2F2 and Myc in hematopoietic differentiation and also to promote keratinocyte differentiation by repressing actin-cytoskeleton regulators PAK4, Tsk5 and ArhGAP19.
Targets of miR-24
Lal et al. suggested that miR-24 suppresses the tumor suppressor p16(INK4a).
Lal et al. reported that mi-24 inhibits cell proliferation by targeting E2F2, MYC via binding to "seedless" 3'UTR microRNA recognition elements.
Amelio I. et al. suggest that miR-24 regulates keratinocyte differentiation, controlling actin-cytoskeleton dynamics via PAK4, Tsk5 and ArhGAP19 repression.
Wang et al. have shown that miR-24 reduces the mRNA and protein levels of human ALK4 by targeting the 3'-untranslated region of mRNA.
Mishra et al. suggest that miR-24 targets the DHFR gene.
miR-24-1, also known as miR-189, targets SLITRK1.
References
External links
miRBase family MIPF0000041
MicroRNA
MicroRN |
https://en.wikipedia.org/wiki/Mir-26%20microRNA%20precursor%20family |
Origins
The miR-26 microRNA is a small non-coding RNA that is involved in regulating gene expression. The miR-26 family is composed of miR-26a-1, miR-26a-2 and miR-26b located in chromosomes 3, 12 and 2, respectively. Pre-miR-26 with stem-loop structure is processed into mature miR-26 by a series of enzymes of intranuclear and intracytoplasm. The mature miRNA of miR-26a-1 and miR-26a-2 possesses the same sequence, with the exception of 2 different nucleotides in mature miR-26b. miR-26 appears to be a vertebrate specific microRNA and has now been predicted or experimentally validated in many vertebrate species (MIPF0000043).
Expressions
miR-26 expression is induced in response to hypoxia and upregulated during smooth muscle cell (SMC) differentiation and neurogenesis. Moreover, miR-26 is consistently down-regulated in a wide range of malignant tumors, such as hepatocellular carcinoma, nasopharyngeal carcinoma, lung cancer, and breast cancer. On the contrary, miR-26a is overexpressed in high-grade glioma and cholangiocarcinoma. Elevated expression of miR-26b has been reported in pituitary tumor and bladder cancer. miR-26 is emerging as critical regulators in carcinogenesis and tumor progression by acting either as oncogenes or tumor suppressor genes in various cancers.
miR-26a roles
Smooth muscle cell (SMC) differentiation
miRNA-26a is found to be significantly upregulated during SMC differentiation and downregulated in abdominal aortic aneurysm (AAA) formation. Inhibition |
https://en.wikipedia.org/wiki/Mir-29%20microRNA%20precursor | The miR-29 microRNA precursor, or pre-miRNA, is a small RNA molecule in the shape of a stem-loop or hairpin. Each arm of the hairpin can be processed into one member of a closely related family of short non-coding RNAs that are involved in regulating gene expression. The processed, or "mature" products of the precursor molecule are known as microRNA (miRNA), and have been predicted or confirmed in a wide range of species (see 'MIPF0000009' in miRBase: the microRNA database).
miRNA processing
Animal miRNAs are first transcribed as a primary miRNA molecule. This "pri-miRNA" may contain one or more precursor hairpins, which are freed from the pri-miRNA by the nuclear enzyme Drosha. The approximately 70 nucleotide precursor hairpin is exported from the nucleus and subsequently processed by the Dicer enzyme to give a mature miRNA that is on average 22 nucleotides long. Either arm of the precursor may yield a mature RNA, although either the 3' (3p) or the 5' (5p) arm is preferentially processed and loaded into the RNA-induced silencing complex (RISC) in most cases. For the miR-29 precursor, the 3' arm of the precursor RNA yields the overwhelmingly predominant product (miR-29 or miR-29-3p), although the 5' arm (miR-29* or miR-29-5p) has also been experimentally verified.
The miR-29 family
Many mammalian genomes encode four closely related miR-29 precursors that are transcribed in two transcriptional units. For example, human miR-29a and miR-29b-1 are processed from an intron of a |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20R105/R108 | In molecular biology, Small nucleolar RNA R105/R108 refers to a group of related non-coding RNA (ncRNA) molecules which function in the biogenesis of other small nuclear RNAs (snRNAs). These small nucleolar RNAs (snoRNAs) are modifying RNAs and usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis.
These two snoRNAs called R105 and R108 were identified in the plant Arabidopsis thaliana and are predicted to belong to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs.
References
External links
plant snoRNA database
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-2%20microRNA%20precursor | The mir-2 microRNA family includes the microRNA genes mir-2 and mir-13 (MIPF0000049). Mir-2 is widespread in invertebrates, and it is the largest family of microRNAs in the model species Drosophila melanogaster. MicroRNAs from this family are produced from the 3' arm of the precursor hairpin. Leaman et al. showed that the miR-2 family regulates cell survival by translational repression of proapoptotic factors. Based on computational prediction of targets, a role in neural development and maintenance has been suggested.
Species distribution
The mir-2 family is specific to protostomes. There are 8 mir-2-related loci in Drosophila melanogaster: mir-2a-1, mir-2a-2, mir-2b-1, mir-2b-2, mir-2c, mir-13a, mir-13b-1 and mir-13b-2. Most other insect genomes host five mir-2 loci although the number varies in other invertebrates. Mir-13 subfamily emerged from mir-2 sequences before the insect radiation.
Although mir-11 and mir-6 have similar sequences to mir-2 microRNAs, they are not evolutionarily related, and therefore should not be considered from the same microRNA family.
Mir-2 hairpin precursor sequences are highly conserved, in particular in their 3' arm in which the first 10 nucleotides are identical to all family members. Functional mir-2 microRNAs come from the 3' arm of the precursors, and most of them have the same Drosha processing point. That means that the seed sequence is virtually the same in all these products, hence, they should target the same transcripts.
Mir-2 m |
https://en.wikipedia.org/wiki/Mir-30%20microRNA%20precursor | miR-30 microRNA precursor is a small non-coding RNA that regulates gene expression. Animal microRNAs are transcribed as pri-miRNA (primary miRNA) of varying length which in turns are processed in the nucleus by Drosha into ~70 nucleotide stem-loop precursor called pre-miRNA (precursor miRNA) and subsequently processed by the Dicer enzyme to give a mature ~22 nucleotide product. In this case the mature sequence comes from both the 3' (miR-30) and 5' (mir-97-6) arms of the precursor. The products are thought to have regulatory roles through complementarity to mRNA.
A screen of 17 miRNAs that have been predicted to regulate a number of breast cancer associated genes found variations in the microRNAs
miR-17 and miR-30c-1, these patients were noncarriers of BRCA1 or BRCA2 mutations, lending the possibility that familial breast cancer may be caused by variation in these miRNAs.
Members of the miR-30 family have been found to be highly expressed in heart cells.
Targets of miR-30
It has been shown that the integrin ITGB3 and the ubiquitin conjugating E2 enzyme UBC9 are downregulated by miR-30. It has also been suggested that the TP53 protein may be a target of miR-30c and miR-30e. An immunoblot analysis revealed that p53 expression levels were elevated upon knockdown of miR-30c and miR-30e.
References
Further reading
External links
MicroRNA |
https://en.wikipedia.org/wiki/Mir-34%20microRNA%20precursor%20family | The miR-34 microRNA precursor family are non-coding RNA molecules that, in mammals, give rise to three major mature miRNAs. The miR-34 family members were discovered computationally and later verified experimentally. The precursor miRNA stem-loop is processed in the cytoplasm of the cell, with the predominant miR-34 mature sequence excised from the 5' arm of the hairpin.
The miR-34 family
In mammals, three miR-34 precursors are produced from two transcriptional units. The human miR-34a precursor is transcribed from chromosome 1. The miR-34b and miR-34c precursors are co-transcribed from a region on chromosome 11, apparently as part of a transcript known as BC021736.
Expression of MIR34A (gene) in mouse is observed in all tissues examined but is highest in brain. miR-34b and -c are relatively less abundant in most tissues, but are the predominant miR-34 species in lung. The presence of miR-34 products has also been confirmed in embryonic stem cells. miR-34 has been shown to be maternally inherited in Drosophila and zebrafish and the loss of miR-34 resulted in defects in hindbrain development in zebrafish embryos. This was the first report of knockdown phenotype of miR-34 in any model organism although the phenotype was observed in only about 30% of zebrafish embryos.
Targets of miR-34
Yamakuchi et al.. showed that miR-34a targets the silent information regulator 1 (SIRT1) gene:
"miR-34 inhibition of SIRT1 leads to an increase in acetylated p53 and expression of p21 and PU |
https://en.wikipedia.org/wiki/Mir-395%20microRNA%20precursor%20family | mir-395 is a non-coding RNA called a microRNA that was identified in both Arabidopsis thaliana and Oryza sativa computationally and was later experimentally verified. mir-395 is thought to target mRNAs coding for ATP sulphurylases. The mature sequence is excised from the 3' arm of the hairpin.
miR-395 is upregulated in Arabidopsis during sulphate-limited conditions, when the mature miRNA then regulates sulphur transporters and ATP sulphurylases.
References
External links
miRBase family entry for mir-395
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20R11/Z151 | In molecular biology, Small nucleolar RNA Z151 (homologous to R11) is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.
snoRNA Z151 belongs to the C/D box class of snoRNAs which contain the conserved sequence motifs known as the C box (UGAUGA) and the D box (CUGA). Most of the members of the box C/D family function in directing site-specific 2'-O-methylation of substrate RNAs
Plant snoRNA Z151 was identified in screens of Oryza sativa
and Arabidopsis thaliana.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-399%20microRNA%20precursor%20family | mir-399 is a microRNA that was identified in both Arabidopsis thaliana and Oryza sativa computationally and was later experimentally verified. mir-399 is thought to target mRNAs coding for a phosphate transporter. The mature sequence is excised from the 3' arm of the hairpin. There are multiple copies of MIR399 in each plant genome, for example A. thaliana contains six microRNA precursors that all give rise to an almost identical mature miR-399 sequence.
References
Further reading
External links
miRBase family MIPF0000015
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Mir-6%20microRNA%20precursor | The mir-6 microRNA precursor is a precursor microRNA specific to Drosophila species. In Drosophila melanogaster there are three mir-6 paralogs called dme-mir-6-1, dme-mir-6-2, dme-mir-6-3, which are clustered together in the genome. The extents of these hairpin precursors are estimated based on hairpin prediction. Each precursor is generated following the cleavage of a longer primary transcript in the nucleus, and is exported in the cytoplasm. In the cytoplasm, precursors are further processed by the enzyme Dicer, generating ~22 nucleotide products from each arm of the hairpin. The products generated from the 3' arm of each mir-6 precursor have identical sequences. Both 5' and 3' mature products are experimentally validated. Experimental data suggests that the mature products of mir-6 hairpins are expressed in the early embryo of Drosophila and target apoptotic genes such as hid, grim and rpr.
Links to further miRNAs
Near perfect complementarity has been observed between miR-5 and miR-6 at 20/21 nucleotides. However, miR-5 is only related on a minor level to any of the three respective miR-6 sequences. miR-6 genes reside in a gene cluster containing other non-K-box family miRNAs, including miRNAs-3 and-309, and the Brd box family gene mir-4. Alignment has shown miR-6 to share the same family motif as miR-11 and miR-2b, together making up the mir-2 clan. There is, however, little similarity in the 3' ends between these clan members.
Apoptotic regulation
mir-6 plays a key ro |
https://en.wikipedia.org/wiki/Mir-7%20microRNA%20precursor | This family represents the microRNA (miRNA) precursor mir-7. This miRNA has been predicted or experimentally confirmed in a wide range of species. miRNAs are transcribed as ~70 nucleotide precursors (modelled here) and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. In this case the mature sequence comes from the 5' arm of the precursor. The extents of the hairpin precursors are not generally known and are estimated based on hairpin prediction. The involvement of Dicer in miRNA processing suggests a relationship with the phenomenon of RNA interference.
Mature miRNA-7 is derived from three microRNA precursors in the human genome, miR-7-1, miR-7-2 and miR-7-3. miRNAs are numbered based on the sequence of the mature RNA.
miR-7 is directly regulated by the transcription factor HoxD10.
miRNAs are thought to have regulatory roles through complementarity to mRNA.
miR-7 is essential for the maintenance of regulatory stability under conditions of environmental flux. It plays an important role in controlling mRNA expression. The miR-7 gene is found in most sequenced Urbilateria species, and the sequence of its mature miRNA product is perfectly conserved from annelids to humans, indicating a strong functional conservation.
Targets of miR-7
Bioinformatic predictions suggest that the human EGFR mRNA 3'-untranslated region contains three microRNA-7 (miR-7) target sites, which are not conserved across mammals. In Drosophila photoreceptor cells, miR-7 cont |
https://en.wikipedia.org/wiki/Mir-92%20microRNA%20precursor%20family | The miR-92 microRNAs are short single stranded non-protein coding RNA fragments initially discovered incorporated into an RNP complex with a proposed role of processing RNA molecules and further RNP assembly. Mir-92 has been mapped to the human genome as part of a larger cluster at chromosome 13q31.3, where it is 22 nucleotides in length but exists in the genome as part of a longer precursor sequence. There is an exact replica of the mir-92 precursor on the X chromosome. MicroRNAs are endogenous triggers of the RNAi pathway which involves several ribonucleic proteins (RNPs) dedicated to repressing mRNA molecules via translation inhibition and/or induction of mRNA cleavage. miRNAs are themselves matured from their long RNA precursors by ribonucleic proteins as part of a 2 step biogenesis mechanism involving RNA polymerase 2.
Most miRNAs are grouped into clusters in the human genome or within families that share functions, expression profiles, promoters, or are incorporated into the same ribonucleic protein. The purpose of having a variety of miRNAs in a single piece of RNA processing machinery is to act as complementary strands to the recognition elements of a variety of target RNA molecules.
The recognition elements of target mRNAs are typically within the 3' untranslated regions and with 678 human miRNAs and 472 mouse miRNAs confidently identified so far (miRBASE) there are extensive efforts taking place using bioinformatics tools to scan genomes for potential recognition |
https://en.wikipedia.org/wiki/Mir-BART1%20microRNA%20precursor%20family | The mir-BART1 microRNA precursor is found in Human herpesvirus 4 (Epstein–Barr virus) and Cercopithicine herpesvirus 15. mir-BART1 is found in all stages of infection but expression is significantly elevated in the lytic stage. In Epstein-Barr virus, mir-BART1 is found in the intronic regions of the BART (Bam HI-A region rightward transcript) gene whose function is unknown. The mature sequence is excised from the 5' arm of the hairpin.
References
External links
MicroRNA
MicroRNA precursor families |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20R30/Z108 | In molecular biology, Small nucleolar RNA R30/Z108 (snoR30) is a C/D box small nucleolar RNA that acts as a methylation guide for 18S ribosomal RNA in plants.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mir-BART2%20microRNA%20precursor%20family | The mir-BART2 microRNA precursor found in Human herpesvirus 4 (Epstein–Barr virus) and Cercopithicine herpesvirus 15. mir-BART2 is expressed in all stages of infection but expression is significantly elevated in the lytic stage. In Epstein-Barr virus, mir-BART2 is found in the intronic regions of the BART (Bam HI-A region rightward transcript) gene whose function is unknown. mir-BART2 is thought to target the virally encoded DNA polymerase BALF5 for degradation. The mature sequence is excised from the 5' arm of the hairpin.
References
External links
VMR_0123 in the VIRmiRNA database
MicroRNA
MicroRNA precursor families |
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