source stringlengths 32 209 | text stringlengths 18 1.5k |
|---|---|
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/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/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-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/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/Kaposi%27s%20sarcoma-associated%20herpesvirus%20internal%20ribosome%20entry%20site%20%28IRES%29 | This family represents the Kaposi's sarcoma-associated herpesvirus (KSHV) internal ribosome entry site (IRES) present in the vCyclin gene. The vCyclin and vFLIP coding sequences are present on a bicistronic transcript and it is thought the IRES may initiate translation of vFLIP from this bicistronic transcript.
References
External links
Cis-regulatory RNA elements |
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-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-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/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-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-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-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/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/Small%20nucleolar%20RNA%20R32/R81/Z41 | In molecular biology, Small nucleolar RNA Z41 (homologous to R32 and R81) 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 Z41 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 Z41 was identified in screens of Arabidopsis thaliana.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Mnt%20IRES | The Mnt internal ribosome entry site (IRES) is an RNA element. Mnt is a transcriptional repressor related to the Myc/Mad family of transcription factors. It is thought that this IRES allows efficient Mnt synthesis when cap-dependent translation initiation is reduced.
See also
N-myc IRES
Tobamovirus IRES
TrkB IRES
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Nanos%203%E2%80%B2%20UTR%20translation%20control%20element | Nanos 3′ UTR translation control element is a cis-regulatory element in the 3′ untranslated region (3′ UTR) of the messenger RNA which encodes the Nanos protein. The Nanos protein in Drosophila is required for correct morphogenesis (anterior/posterior patterning) in the Drosophila embryo. Translation of the Nanos mRNA is repressed in the bulk cytoplasm and activated in the posterior region. The translation control element (TCE) in the 3'UTR forms a Y-shaped secondary structure, part of which is recognised by the Smaug protein and leads to translational repression.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/N-myc%20internal%20ribosome%20entry%20site%20%28IRES%29 | The N-myc internal ribosome entry site (IRES) is an RNA element found in the n-myc gene. The myc family of genes when expressed are known to be involved in the control of cell growth, differentiation and apoptosis. n-myc mRNA has an alternative method of translation via an internal ribosome entry site where ribosomes are recruited to the IRES located in the 5' UTR thus bypassing the typical eukaryotic cap-dependent translation pathway.
See also
Mnt IRES
Tobamovirus IRES
TrkB IRES
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Nuclear%20RNase%20P | In molecular biology, nuclear ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised enzyme activity is the generation of mature 5′-ends of tRNAs by cleaving the 5′-leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. The RNA from bacterial RNase P retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Similarly, archaeal RNase P RNA has been shown to be weakly catalytically active in the absence of its respective protein cofactors. Isolated eukaryotic RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all three lineages are homologous—the helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet there is considerable sequence variation, particularly among the eukaryotic RNAs.
References
Further reading
External links
RNase P
Non-coding RNA |
https://en.wikipedia.org/wiki/OxyS%20RNA | OxyS RNA is a small non-coding RNA which is induced in response to oxidative stress in Escherichia coli. This RNA acts as a global regulator to activate or repress the expression of as many as 40 genes, by an antisense mechanism, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. Binding to Hfq alters the conformation of OxyS. The 109 nucleotide RNA is thought to be composed of three stem-loops.
Target genes
A number of additional targets were predicted and verified using microarray analysis. These are listed below:
yobF – confirmed by Northern analysis
yaiZ
rumA
wrbA – confirmed by Northern analysis
ybaY – confirmed by Northern analysis
Furthermore, the mRNA encoded by the nusG gene is a direct target of OxyS.
References
External links
OxyS entry in the ncRNA database
Non-coding RNA |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20R44/J54/Z268%20family | In molecular biology, Small nucleolar RNA R44/J54/Z268 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 are usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis.
These snoRNAs appear plant-specific and were identified in Arabidopsis thaliana and rice Oryza sativa (snoRNAs Z268 and J54). These related snoRNAs 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/P27%20cis-regulatory%20element | The p27 cis-regulatory element is a structured G/C rich RNA element which is involved in controlling cell cycle regulated translation of the p27kip protein in human cells.
The p27kip1 protein is involved in cell cycle regulation and belongs to the Cip/Kip family of cyclin dependent kinase(CDK)inhibitors. These inhibitors possess an N-terminal CDK-inhibitory domain which binds to the ATP binding pocket of the kinase and modulates its function.
This p27 cis-regulatory element is 114 nucleotides in length and is located at the very 5' end of the 5'UTR of the p27 mRNA. It contains a small open reading frame (ORF) of 29 amino acids which is preceded by and overlaps with a G/C-rich hairpin domain. This hairpin domain is predicted to form multiple stable stem loops with similar free energy. Both the open reading frame and the stem loop elements contribute to cell cycle-regulated translation of the p27 mRNA.
The structure of the G/C rich element appears to be important to its regulatory function as replacement of the G/C rich region with an unstructured sequence has a greater effect on regulation of translation than a simple deletion of part of the G/C rich region. It has been suggested that cell cycle specific binding proteins may favour one of the predicted structures in the G/C region thereby promoting conformational states which could regulate downstream translation.
This element was initially characterised in human cells but has predicted homologs in mice and chickens.
Ref |
https://en.wikipedia.org/wiki/Pestivirus%20internal%20ribosome%20entry%20site%20%28IRES%29 | This family represents the internal ribosome entry site (IRES) of the pestiviruses. The pestivirus IRES allows cap and end-independent translation of mRNA in the host cell. The IRES achieves this by mediating the internal initiation of translation by recruiting a ribosomal 43S pre-initiation complex directly to the initiation codon and eliminates the requirement for the eukaryotic initiation factor, eIF4F. The classical swine fever virus UTR described appears to be longer at the 5' end than other pestivirus UTRs. This family represents the conserved core.
References
External links
Cis-regulatory RNA elements
Internal ribosome entry site |
https://en.wikipedia.org/wiki/Picornavirus%20internal%20ribosome%20entry%20site%20%28IRES%29 | This family represents the Picornavirus internal ribosome entry site (IRES) element present in their 5' untranslated region. These elements were discovered in picornaviruses. They are cis-acting RNA sequences that adopt diverse three-dimensional structures, recruit the translation machinery and that often operate in association with specific RNA-binding proteins. IRES elements allow cap and end-independent translation of mRNA in the host cell. It has been found that La autoantigen (La) is required for Coxsackievirus B3 (CVB3) IRES-mediated translation, and it has been suggested that La may be required for the efficient translation of the viral RNA in the pancreas. Based on their secondary structure, picornavirus IRES are grouped into four main types. Type I comprises enteroand rhinovirus IRES and type II, those of cardio- and aphthovirus, among others. Type III is used to name hepatitis A IRES.
References
External links
http://rfam.xfam.org/family/RF00229 Picornavirus internal ribosome entry site (IRES)
Cis-regulatory RNA elements
Internal ribosome entry site
Picornaviridae |
https://en.wikipedia.org/wiki/Plant%20small%20nucleolar%20RNA%20R71 | In molecular biology, small nucleolar RNA R71 (also known as snoRNA R71) 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.
R71 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.
Multiple, nearly identical copies of this snoRNA have been identified in the Arabidopsis thaliana genome and it is thought to function as a 2'-O-ribose methylation guide for 18S ribosomal RNA (rRNA).
References
External links
plant snoRNA database
Small nuclear RNA |
https://en.wikipedia.org/wiki/Plasmid%20RNAIII | Plasmid RNAIII is a non-coding RNA found in bacterial plasmids including pIP501. RNAIII acts by transcriptional attenuation of the essential repR-mRNA. RNAIII is composed of four stem-loops with loops L3 and L4 that interact with the RNA target.
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20R64/Z200%20family | In molecular biology, R64/Z200 is a member of the C/D class of small nucleolar RNA which guide the site-specific 2'-O-methylation of substrate RNA. This family can be found in Arabidopsis thaliana (R64) and Oryza sativa (Z200).
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/Pospiviroid%20RY%20motif%20stem%20loop | The Pospiviroid RY motif stem loop is an RNA element found in Pospiviroids such as potato spindle tuber viroid (PSTVd). The RY nucleotide sequence motif (5'-ACAGG and CUCUUCC-5') in PSTVd, is thought to bind with the tomato protein Virp1. The exact function of this motif and the significance of Virp1 binding is unknown. It is however thought that RY motifs are essential for establishing a viroid infection.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Potassium%20channel%20RNA%20editing%20signal | The potassium channel RNA editing signal is an RNA element found in human Kv1.1 and its homologues which directs the efficient modification of an adenosine to inosine by an adenosine deaminase acting on RNA (ADAR). The ADAR modification causes an isoleucine/valine recoding event which lies in the ion-conducting pore of the potassium channel. It is thought that this editing event targets the process of fast inactivation and allows a more rapid recovery from inactivation at negative potentials.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Potato%20virus%20X%20cis-acting%20regulatory%20element | The Potato virus X cis-acting regulatory element is a cis-acting regulatory element found in the 3' UTR of the Potato virus X genome. This element has been found to be required for minus strand RNA accumulation and is essential for efficient viral replication.
See also
Poxvirus AX element late mRNA cis-regulatory element
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20snoR31/Z110/Z27 | In molecular biology, Small nucleolar RNA Z110 (homologous to Z27 and R31) 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 Z110 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 Z110 was identified in screens of Arabidopsis thaliana and
Oryza sativa
.
References
External links
Small nuclear RNA |
https://en.wikipedia.org/wiki/PrfA%20thermoregulator%20UTR | The PrfA thermoregulator UTR is an RNA thermometer found in the 5' UTR of the prfA gene. In Listeria monocytogenes, virulence genes are maximally expressed at 37 °C (human body temperature) but are almost silent at 30 °C. The genes are controlled by PrfA, a transcriptional activator whose expression is thermoregulated. It has been shown that the untranslated mRNA (UTR) preceding prfA, forms a secondary structure, which masks the ribosome binding region. It is thought that at 37 °C, the hairpin structure 'melts' and the SD sequence is unmasked.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Prion%20pseudoknot | The prion pseudoknot is predicted RNA pseudoknot structure found in prion protein mRNA. It has been suggested that this element has a possible effect in prion protein translation. The human prion protein gene contains 5 copies of a 24 nucleotide repeat that contains this structure. The number of nucleotide repeats found in an organism may vary from one organism to another. Each species has a set number of nucleotide repeats, but when the organism deviates from this number, mutations in the prion genes may arise. Human individuals that exhibit these mutations may be prone to developing prion diseases, such as Creutzfeldt-Jakob disease.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/PrrF%20RNA | The PrrF RNAs are small non-coding RNAs involved in iron homeostasis and are encoded by all Pseudomonas species. The PrrF RNAs are analogs of the RyhB RNA, which is encoded by enteric bacteria. Expression of the PrrF RNAs is repressed by the ferric uptake regulator (Fur) when cells are grown in iron-replete conditions. Under iron limitation, the PrrF RNAs are expressed and act to negatively regulate several genes encoding iron-containing proteins, including SodB and succinate dehydrogenase. As such, PrrF regulation "spares" iron when this nutrient becomes scarce.
PrrF and virulence
In Pseudomonas aeruginosa, the PrrF RNAs are required for the production of the Pseudomonas quinolone signal (PQS), a quorum sensing molecule that activates the expression of several virulence genes. The phenomenon is mediated by PrrF repressing the expression of enzymes that degrade anthranilic acid, which is the precursor for PQS synthesis. Due to this regulatory link with PQS, the PrrF RNAs are predicted to play a role in pathogenesis.
The PrrF RNAs of P. aeruginosa are unique from other Pseudomonas species, in that they are encoded by two highly homologous genes, prrF1 and prrF2, which are located in tandem on the chromosome. The tandem arrangement of the prrF genes allows for the expression of a third, heme-regulated non-coding RNA named PrrH, which regulates genes involved in heme homeostasis. Heme is an abundant source of iron in the human host, and P. aeruginosa is the only Pseudomonas s |
https://en.wikipedia.org/wiki/Purine%20riboswitch | A purine riboswitch is a sequence of ribonucleotides in certain messenger RNA (mRNA) that selectively binds to purine ligands via a natural aptamer domain. This binding causes a conformational change in the mRNA that can affect translation by revealing an expression platform for a downstream gene, or by forming a translation-terminating stem-loop. The ultimate effects of such translational regulation often take action to manage an abundance of the instigating purine, and might produce proteins that facilitate purine metabolism or purine membrane uptake.
Binding properties
Purine riboswitches bind to their purine ligands via interactions at a three-way junction formed by junctional helix P1 and hairpin helices P2 and P3. Associations that a purine makes when it is within this binding pocket stabilize the three-way junction, and support the ligand-bound conformation of the mRNA molecule. The purine riboswitch can become saturated at concentrations as low as 5 nM, which reflects the need for gene expression to respond quickly and dynamically to changes in purine concentration.
Despite the relative similarity of the purine-binding aptamer domain across different purine riboswitches, one binding pocket can still discriminate for a single type of purine ligand with high selectivity. Critical to this sensitivity is a single difference in the secondary structure of ribonucleotides: in position 74 of the aptamer domain, it has been found that conversion of a cytosine to a uracil |
https://en.wikipedia.org/wiki/PyrR%20binding%20site | The PyrR binding site is an RNA element that is found upstream of a variety of genes involved in pyrimidine biosynthesis and transport.
The RNA structure permits binding of PyrR protein which regulates pyrimidine biosynthesis in Bacillus subtilis. When the protein binds, a downstream terminator hairpin forms, repressing transcription of biosynthesis genes.
References
External links
Cis-regulatory RNA elements |
https://en.wikipedia.org/wiki/Anti-Q%20RNA | Anti-Q RNA (formerly Qa RNA) is a small ncRNA from the conjugal plasmid pCF10 of Enterococcus faecalis. It is coded in cis to its regulatory target, prgQ, but can also act in trans. Anti-Q is known to interact with nascent prgQ transcripts to allow formation of an intrinsic terminator, or attenuator, thus preventing transcription of downstream genes. This mode of regulation is essentially the same as that of the countertranscript-driven attenuators that control copy number in pT181, pAMbeta1 and pIP501 and related Staphylococcal plasmids.
Anti-Q is transcribed from the same segment of DNA as prgQ, except from the opposite strand, making it perfectly complementary to a portion of prgQ. Further experiments have experimentally confirmed the original consensus secondary structure and demonstrated that only certain regions of Anti-Q interact with prgQ.
Anti-Q is derived from the 5’ end a longer transcript. The 3’ end of this transcript encodes PrgX, a repressor of prgQ transcription.
References
External links
Non-coding RNA |
https://en.wikipedia.org/wiki/Qrr%20RNA |
Introduction
Qrr (Quorum regulatory RNA) is a small non-coding RNA that is thought to be involved in the regulation of quorum sensing in Vibrio species. The use of small RNAs for vital functions like metabolism, infection cycling, and stress response is ubiquitous among bacteria. Qrr operates as part of a negative feedback loop which regulates the shift in cell state from that of low density populations to that in high density populations. This feedback system allows for rapid responses to changes in population cell density, eliminating the production of energy-costly molecules. It is believed that these RNAs, guided by a protein, Hfq, can mediate the destabilization of the quorum-sensing master regulators LuxR/HapR/VanT mRNAs. This group of non-coding RNAs are trans-acting small RNAs (sRNAs) that bind via base pairing to the untranscribed domain of their mRNA targets. This binding results in degradation or stabilization, deciding their translational fate.
Qrr RNA Characteristics
Genes, Expression, and Mechanism
There are 5 different qrr genes (Qrr1–5) in V. harveyi; of these, qrr2, 3 and 4 are activated by LuxR. Other Vibrio species contain varying number of these genes, with overlapping functions and promotion. Each of these Qrr RNAs are expressed at different times, fluctuating in level. Each gene is expressed individually based on growth conditions, with unique factors and regulators controlling their respective expression. For example, LuxT transcriptionally repres |
https://en.wikipedia.org/wiki/Sib%20RNA | Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib (for short intergenic abundant sequences) when it was discovered that the number of repeats is variable in other species and in other E. coli strains.
Identification
These small RNA were identified computationally by searching the genome of E. coli for intergenic regions of high sequence identity (sequence conservation) with the genomes of closely related bacteria (several salmonella species and Klebsiella pneumoniae). This data was combined with microarray expression analysis and potential novel ncRNAs identified. The expression of novel ncRNA of interest was confirmed by northern blotting.
In this large scale screen these ncRNAs were simply referred to as candidates 43, 55 and 61. These 3 ncRNA appear to be highly homologous and are derived from a repeat region of the genome. Each of the ncRNA contains a short stretch homologous to boxC, a repeat element of unknown function present in 50 copies or more within the genome of E. coli.
Function
Sib RNA regulates the expression of a toxic protein in a type I toxin-antitoxin system similar to that of hok/sok andldr-rdl genes. The constitutively expressed Sib transcript regulates the ibs (induction brings stasis) open reading frame which encodes a small 18–19 amino acid hydrophobic protein which slows growth at mode |
https://en.wikipedia.org/wiki/R1162-like%20plasmid%20antisense%20RNA | R1162-like plasmid antisense RNA is a 75-base RNA molecule which negatively regulates the RepI region of the plasmid. The protein product of this gene region, along with another protein, controls the copy number of the 8.75kB R1162 plasmid.
Experimental evidence has shown that in Escherichia coli, when levels of this RNA are decreased, the plasmid copy number of R1162 is increased.
References
External links
Antisense RNA |
https://en.wikipedia.org/wiki/R2%20RNA%20element | The R2 RNA element is a non-long terminal repeat (non-LTR) retrotransposable element that inserts at a specific site in the 28S ribosomal RNA (rRNA) genes of most insect genomes. In order to insert itself into the genome, retrotransposon encoded protein (R2) protein makes a specific nick in one of the DNA strands at the insertion site and uses the 3′ hydroxyl group exposed by this nick to prime the reverse transcription process termed target primed reverse transcription (TPRT), where the RNA genome is transcribed into DNA.
3' UTR element
The R2 element 3' UTR RNA is a cis-acting element identified in R2 retrotransposons which is involved in priming the reverse transcription process (an essential part of retrotransposon insertion into the host genome). An RNA fragment found in the R2 3' untranslated region (3'UTR), has been shown to interact with one copy of R2 protein during TPRT. This fragment has been shown to possess conserved secondary structure within Drosophila and silk moths, and also between the two groups.
5' UTR ribozyme
The R2 element is co-transcribed with host organism 28S ribosomal RNA (rRNA). To become a fully mature R2 messenger RNA (mRNA), requires that the initial R2 transcript be processed to remove the 28S rRNA. This processing occurs via a self-cleaving ribozyme that forms at the 5' junction of the R2 RNA. This ribozyme has been found to have high structural similarity to the HDV ribozyme but they are not homologous; the two sequences are thought to ha |
https://en.wikipedia.org/wiki/Small%20nucleolar%20RNA%20snoR639/H1 | In molecular biology, Small nucleolar RNA snoR639 (also known as snoH1) is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is 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'.
snoR639 was originally identified in a study of Drosophila melanogaster minifly (mfl) gene; snoR639 resides in the intron of this gene. It was later rediscovered by a large-scale RNomics effort.
snoR639 belongs to the H/ACA box class of snoRNAs as it has the predicted hairpin-hinge-hairpin-tail structure, has the conserved H/ACA-box motifs and is found associated with GAR1 protein.
References
External links
Small nuclear RNA |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.