abstract string | rna_related int64 |
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although microrna-144-3p (mirna-144-3p) has been shown to suppress tumor proliferation and invasion, its function in intracerebral hemorrhage (ich)-induced secondary brain injury (sbi) remains unclear. thus, this study was designed to investigate the role of mirna-144-3p in ich. to accomplish this, we used adult male s... | 1 |
a mutation located in the 5'-untranslated region (5'-utr) of the nerve-specific connexin-32 mrna, previously found in a family with charcot-marie-tooth disease (cmtx), was analyzed for its effect on the expression of a reporter gene (luciferase) in transgenic mice and in transfected cells. whereas both mutant and wild-... | 1 |
background micrornas (mirnas) are short, non-coding rnas (~22 nt) that play important roles in the pathogenesis of human diseases by negatively regulating gene expression. although mir-196a has been implicated in several other cancers, its role in non-small cell lung cancer (nsclc) is unknown. the aim of the present st... | 1 |
here we describe a set of endogenous short interfering rnas (sirnas) in arabidopsis, some of which direct the cleavage of endogenous mrnas. these sirnas correspond to both sense and antisense strands of a noncoding rna (at2g27400) that apparently is converted to double-stranded rna and then processed in 21 nt increment... | 1 |
in saccharomyces cerevisiae, seven snrnas (snr3, 4, 5, 8, 9, 10 and 17) are retained in the nucleus under conditions in which nucleoplasmic rnas are lost, and may be nucleolar. all of these snrnas show properties consistent with hydrogen bonding to pre-ribosomal rnas; snr5 and 8 with 20s pre-rrna, snr3, 4, 10 and 17 wi... | 1 |
micrornas are short, endogenous non-coding rnas that act as post-transcriptional modulators of gene expression. important functions for micrornas have been found in the regulation of development, cellular proliferation and differentiation, while perturbed mirna expression patterns have been observed in many human cance... | 1 |
fsh plays an essential role in processes involved in human reproduction, including spermatogenesis and the ovarian cycle. while the transcriptional regulatory mechanisms underlying its synthesis and secretion have been extensively studied, little is known about its posttranscriptional regulation. a bioinformatics analy... | 1 |
progressive hearing loss is common in the human population, but little is known about the molecular basis. we report a new n-ethyl-n-nitrosurea (enu)-induced mouse mutant, diminuendo, with a single base change in the seed region of mirn96. heterozygotes show progressive loss of hearing and hair cell anomalies, whereas ... | 1 |
nodal is a member of the transforming growth factor-β superfamily that plays crucial roles during embryogenesis. recently, we have reported that nodal inhibits trophoblast cell proliferation, migration and invasion, but induces apoptosis in the human placenta. in this study, we examined the regulation of nodal by micro... | 1 |
background micrornas (mirnas) are endogenous, small non-coding rnas that play important roles in multiple biological processes. mir-20b has been reported to participate in breast cancer tumorigenic progression, however, the functional roles are still unclear and under debating. the aim of this study is to explicit the ... | 1 |
the mir-302-367 cluster is specifically expressed in human embryonic stem cells and has been shown to convert human somatic cells into induced pluripotent stem cells. here, we investigated the role of the mir-302-367 cluster in cervical carcinoma. the cluster was not endogenously expressed in cervical cancer cells, and... | 1 |
morphogenesis is crucial to initiate physiological development and tumor invasion. here we show that a microrna controls zonation morphogenesis by targeting hyaluronan receptor cd44. we have developed a novel system to study microrna functions by generating constructs expressing pre-mirnas and mature mirnas. using this... | 1 |
given that mir-124 is preferentially expressed in differentiating and mature neurons and external granule cells of cerebellum are thought to be cells-of-origins of medulloblastomas, we investigated if mir-124 played a role in the development of medulloblastomas. quantitative expression analysis of 29 medulloblastomas d... | 1 |
relatively little is known about the evolutionary histories of most classes of non-protein coding rnas. here we consider y rnas, a relatively rarely studied group of related pol-iii transcripts. a single cluster of functional genes is preserved throughout tetrapod evolution, which however exhibits clade-specific tandem... | 1 |
spaced synaptic depolarization induces rapid axon terminal growth and the formation of new synaptic boutons at the drosophila larval neuromuscular junction (nmj). here, we identify a novel presynaptic function for the calcium/calmodulin-dependent kinase ii (camkii) protein in the control of activity-dependent synaptic ... | 1 |
micrornas (mirnas) are thought to have an important role in tumor metastasis by regulating diverse cellular pathways. here, we describe the function and regulation network of mir-206 in gastric cancer (gc) metastasis. mir-206 expression was downregulated in gc cells especially in high metastatic potential cells and was... | 1 |
micrornas (mirnas) are short noncoding rna molecules, which posttranscriptionally regulate genes expression and play crucial roles in diverse biological processes, such as development, differentiation, apoptosis and proliferation. here, we investigated the possible role of mirnas in the development of multidrug resista... | 1 |
hepatic scavenger receptor class b type i (sr-bi) plays an important role in selective high-density lipoprotein cholesterol (hdl-c) uptake, which is a pivotal step of reverse cholesterol transport. in this study, the potential involvement of micrornas (mirnas) in posttranscriptional regulation of hepatic sr-bi and sele... | 1 |
ribonuclease p (rnase p) is a ribonucleoprotein enzyme that cleaves precursor trna transcripts to give mature 5' ends. rnase p in eubacteria has a large, catalytic rna subunit and a small protein subunit that are required for precursor trna cleavage in vivo. although the eukaryotic holoenzymes have similar, large rna s... | 1 |
animal microrna (mirna) target prediction is still a challenge, although many prediction programs have been exploited. mirnas exert their function through partially binding the messenger rnas (mrnas; likely at 3' untranslated regions ), which makes it possible to detect the mirna-mrna interactions in vitro by co-transf... | 1 |
there has been a great expansion in the number of small regulatory rnas identified in bacteria. some of these small rnas repress the synthesis of potentially toxic proteins. generally the toxin proteins are hydrophobic and less than 60 amino acids in length, and the corresponding antitoxin small rna genes are antisense... | 1 |
pkr, an interferon (ifn)-inducible protein kinase activated by double-stranded rna, inhibits translation by phosphorylating the initiation factor eif2alpha chain. we show that human ifn-gamma mrna uses local activation of pkr in the cell to control its own translation yield. ifn-gamma mrna activates pkr through a pseud... | 1 |
a 190-nucleotide (nt) packaging signal (ps) located in the 3' end of open reading frame 1b in the mouse hepatitis virus, a group iia coronavirus, was previously postulated to direct genome rna packaging. based on phylogenetic data and structure probing, we have identified a 95-nt hairpin within the 190-nt ps domain whi... | 1 |
purpose microrna-21 (mirna-21) has proto-oncogenic properties, although no mirna-21-specific targets have been found in head and neck squamous cell carcinoma (hnscc). further study of mirna-21 and its specific targets is essential to understanding hnscc biology. experimental design mirna expression profiles of 10 hnscc... | 1 |
micrornas (mirnas) are essential components of gene regulation, but identification of mirna targets remains a major challenge. most target prediction and discovery relies on perfect complementarity of the mirna seed to the 3' untranslated region (utr). however, it is unclear to what extent mirnas target sites without s... | 1 |
the quest for non-coding rnas (ncrnas) in the last few years has revealed a surprisingly large number of small rnas belonging to previously known as well as entirely novel classes. computational and experimental approaches have uncovered new ncrnas in all kingdoms of life. in this work, we used a shotgun cloning approa... | 1 |
mir-185 expression has been associated with many cancers. however, the roles of mir-185 in human breast cancer remain elusive. here, we found that mir-185 expression was decreased in human breast cancer tissues compared with healthy tissue controls. up-regulation of mir-185 inhibited breast cancer cell proliferation an... | 1 |
7sk rna is a highly abundant noncoding rna in mammalian cells whose function in transcriptional regulation has only recently been elucidated. despite its highly conserved sequence throughout vertebrates, all attempts to discover 7sk rna homologues in invertebrate species have failed so far. here we report on a combined... | 1 |
micrornas (mirnas) play critical roles in retinoblastoma (rb) initiation and progression, aberrant expression of mir-145 had been frequently reported in cancer studies. however, the role and mechanism of its function in rb is still unclear. in this study, our data showed that mir-145 was downregulated in rb tissues and... | 1 |
hodgkin lymphoma (hl) is derived from preapoptotic germinal center b cells, although a general loss of b cell phenotype is noted. using quantitative reverse transcription-polymerase chain reaction and mirna microarray, we determined the microrna (mirna) profile of hl and compared this with the profile of a panel of b-c... | 1 |
gata-4 is an important transcription factor involved in several developmental processes of the heart, such as cardiac myocyte proliferation, differentiation and survival. the precise mechanisms underlying the regulation of gata-4 remain unclear, this is especially true for the mechanisms that mediate the post-transcrip... | 1 |
how mirnas recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. several features, such as perfect pairing of the mirna seed, additional pairing in the 3' region of the mirna, relative position in the 3' utr, and the a/u content of the environment of the putative site... | 1 |
aberrant expression of dna polymerase beta, a key enzyme involved in base excision repair, leads to genetic instability and carcinogenesis. pol beta expression has been previously shown to be regulated at the level of transcription, but there is also evidence of post-transcriptional regulation, since rat transcripts un... | 1 |
the currently available yeast mitochondrial dna (mtdna) sequence is incomplete, contains many errors and is derived from several polymorphic strains. here, we report that the mtdna sequence of the strain used for nuclear genome sequencing assembles into a circular map of 85,779 bp which includes 10 kb of new sequence. ... | 1 |
polycomb group (pcg) proteins exert essential functions in the most disparate biological processes. the contribution of pcg proteins to cell commitment and differentiation relates to their ability to repress transcription of developmental regulators in embryonic stem (es) cells and in committed cell lineages, including... | 1 |
previously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preq1). the enormous expansion of available genomic dna sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover nove... | 1 |
5s rrna extends from the central protuberance of the large ribosomal subunit, through the a-site finger, and down to the gtpase-associated center. here, we present a structure-function analysis of seven 5s rrna alleles which are sufficient for viability in the yeast saccharomyces cerevisiae when expressed in the absenc... | 1 |
recent studies suggest that microrna (mirna) plays important roles in the control of immune response and tolerance. we previously found that the expression level of antimicrobial peptide gene drosomycin (drs) is decreased in mir-964 overexpressing flies. here, we further verified that mir-964 deficiency leads to hyper-... | 1 |
micrornas (mirna) regulate complex patterns of gene expression, and the relevance of altered mirna expression to ovarian cancer remains to be elucidated. by comprehensively profiling expression of mirnas and mrnas in serous ovarian tumors and cell lines and normal ovarian surface epithelium, we identified hundreds of p... | 1 |
the regulation of function of endothelial cell-cell junctions is fundamental in sustaining vascular integrity. the polycistronic microrna (mir) complexes containing mir-23a-27a-24-2, and 23b-27b-24-1 are predicted to target the majority of major endothelial junctional proteins. we focus on mir-23a and mir-23b, and inve... | 1 |
bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. one of these motifs is found exclusively in the family streptococcaceae within the 5' untranslated regions (utrs) of genes encoding the h... | 1 |
many or all of the sites of pseudouridine (psi) formation in eukaryotic rrna are selected by site-specific base-pairing with members of the box h + aca class of small nucleolar rnas (snornas). database searches previously identified strong homology between the rat nucleolar protein nap57p, its yeast homolog cbf5p, and ... | 1 |
mir-7 (microrna-7) has been characterized as a tumour suppressor in several human cancers. it targets a number of proto-oncogenes that contribute to cell proliferation and survival. however, the mechanism(s) by which mir-7 suppresses tumorigenesis in tscc (tongue squamous cell carcinoma) is unknown. the present bioinfo... | 1 |
sensorineural hearing loss (snhl) is the most common cause of hearing impairment. one of the essential steps to prevent progressive hearing loss is to protect spiral ganglion neurons (sgns) from ongoing degeneration. micrornas and tmprss3 (transmembrane protease, serine 3) have been reported to be involved in developme... | 1 |
streptomyces are predominantly soil-dwelling bacteria that are best known for their multicellular life cycle and their prodigious metabolic capabilities. they are also renowned for their regulatory capacity and flexibility, with each species encoding >60 sigma factors, a multitude of transcription factors, and an incre... | 1 |
mirnas can have pleiotropic effects by targeting multiple genes belonging to diverse signalling networks. alternatively, mirnas can enhance the potency of their cellular effects by targeting multiple genes within the same genetic pathway. previously, we and others have demonstrated that mir-335 is a potent suppressor o... | 1 |
aim microangiopathy due to endothelial dysfunction is a major contributing factor to the development of diabetes-induced cardiovascular disease (cvd). dysregulation of endothelial-specific micrornas (mirs) is correlated with impaired angiogenesis and cell survival. we investigated the profile of two angiomirs, mir-126,... | 1 |
toll-like receptors (tlrs) are important pathogen recognition molecules and are key to epithelial immune responses to microbial infection. however, the molecular mechanisms that regulate tlr expression in epithelia are obscure. micro-rnas play important roles in a wide range of biological events through post-transcript... | 1 |
microrna 21 (mir-21) has been implicated in various aspects of carcinogenesis. however, its function and molecular mechanism in cervical squamous carcinoma have not been studied. using taqman quantitative real-time pcr and northern blot, we confirmed that mir-21 is significantly overexpressed in human cervical squamous... | 1 |
nidoviruses produce an extensive 3'-coterminal nested set of subgenomic mrnas, which are used to express their structural proteins. in addition, arterivirus and coronavirus mrnas contain a common 5' leader sequence, derived from the genomic 5' end. the joining of this leader sequence to different segments (mrna bodies)... | 1 |
micrornas (mirnas) are a class of 20-24 nt non-coding rnas that regulate gene expression primarily through post-transcriptional repression or mrna degradation in a sequence-specific manner. the roles of mirnas are just beginning to be understood, but the study of mirna function has been limited by poor understanding of... | 1 |
hedgehog (hh) pathway signaling is crucial for the maintenance of blood cell progenitors in the lymph gland hematopoietic organ present in drosophila third instar larvae. previous studies from our lab have likewise shown the importance of the mir-7 and bag of marbles (bam) genes in maintaining the progenitor state. thu... | 1 |
although there is abundant evidence that individual microrna (mirna) loci repress large cohorts of targets, large-scale knockout studies suggest that most mirnas are phenotypically dispensable. here, we identify a rare case of developmental cell specification that is highly dependent on mirna control of an individual t... | 1 |
notch (n) signaling is central to the self-renewal of neural stem cells (nscs) and other tissue stem cells. its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases. how n regulates stem cell behavior in health and disease is not well understood. here we show that n regulates ... | 1 |
lung cancer is the most common type of cancer-related death in developed countries. micrornas (mirnas) are small non-coding rnas, which regulates gene expression in cancer. recent studies demonstrate that the microrna-293-3p (mir-293-3p) may play as an oncogene or a tumor suppressor. however, its expression and roles i... | 1 |
objective abdominal aortic aneurysm (aaa) is characterized as a progressive dilation and degradation of the aortic wall, associated with activation of matrix metalloproteinases (mmps) and inflammation. emerging evidence indicates a role for micrornas (mirnas) in aaa pathogenesis, but it is unclear whether abdominal aor... | 1 |
cutaneous homeostasis and innate immunity is procured by a complex circuitry of intercellular cytokine signaling. micrornas are important posttranscriptional regulators of keratinocyte gene expression and assist in modulating the fine balance between cell proliferation and differentiation in skin. a characteristic micr... | 1 |
rna-based therapeutics are emerging as innovative options for cancer treatment, with micrornas being attractive targets for therapy development. we previously implicated microrna-642a-5p (mir-642a-5p) as a tumor suppressor in prostate cancer (pca), and here we characterize its mode of action, using 22rv1 pca cells. in ... | 1 |
co(2) sensation represents an interesting example of nervous system and behavioral evolutionary divergence. the underlying molecular mechanisms, however, are not understood. loss of microrna-279 in drosophila melanogaster leads to the formation of a co(2) sensory system partly similar to the one of mosquitoes. here, we... | 1 |
spontaneous self-terminating atrial fibrillation (af) is one of the most common heart rhythm disorders, yet the regulatory molecular mechanisms underlying this syndrome are rather unclear. microrna (mirna) transcriptome and expression of candidate transcription factors (tfs) with potential roles in arrhythmogenesis, su... | 1 |
background/aims the objective of this study was to investigate the potential role of il-17 in the development of nasopharyngeal carcinoma (npc) and to screen micrornas (mirnas) that potentially target il-17 in npc cells. methods blood was collected from npc patients and normal subjects, and plasma il-17 concentration w... | 1 |
x inactivation is controlled by xist and its antisense gene, tsix, neither of which encodes a protein. xist is essential for x inactivation to occur in cis, and its differential expression is a key event in the initiation of x inactivation. xist and tsix are imprinted in the extraembryonic tissues of mouse embryos so t... | 1 |
chronic infection with hepatotropic viruses is the main cause of chronic liver disease and cirrhosis worldwide. toll-like receptor 3 (tlr3) and toll-like receptor 7 (tlr7) are pathogen-recognition receptors that are expressed on innate immune cells. they recognize viral rna, which induces their activation, with a subse... | 1 |
akt2 is a crucial mediator in the tumorigenesis and thought to be an ideal target for the treatment of malignancies. increasing evidence has also shown that micrornas (mirnas) could regulate or be regulated by mrnas and they also might serve as therapeutic agencies or targets. mir-29s (mir-29a, mir-29b and mir-29c) had... | 1 |
rationale viral myocarditis results from an adverse immune response to cardiotropic viruses, which causes irreversible myocyte destruction and heart failure in previously healthy people. the involvement of micrornas and their usefulness as therapeutic targets in this process are unknown. objective to identify micrornas... | 1 |
background myocardial infarction leads to cardiac remodeling and development of heart failure. insufficient myocardial capillary density after myocardial infarction has been identified as a critical event in this process, although the underlying mechanisms of cardiac angiogenesis are mechanistically not well understood... | 1 |
three elements are crucial for the programmed frameshifting in translation of dnax mrna: a shine-dalgarno (sd)-like sequence, a double-shift site, and a 3' structure. the conformation of the mrna containing these three elements was investigated using chemical and enzymatic probes. the probing data show that the structu... | 1 |
msx1 is a key factor for the development of tooth and craniofacial skeleton and has been proposed to play a pivotal role in terminal cell differentiation. in this paper, we demonstrated the presence of an endogenous msx1 antisense rna (msx1-as rna) in mice, rats, and humans. in situ analysis revealed that this rna is e... | 1 |
objective single nucleotide polymorphisms (snps) located at microrna (mirna) binding sites (mir-snps) can affect the expression of genes. this study aimed to identify the mir-snps associated with atherosclerosis and stroke. methods patients with ischemic stroke (n = 657) and stroke- and myocardial infarction-free volun... | 1 |
brca1, a breast and ovarian tumor suppressor, colocalizes with markers of the inactive x chromosome (xi) on xi in female somatic cells and associates with xist rna, as detected by chromatin immunoprecipitation. breast and ovarian carcinoma cells lacking brca1 show evidence of defects in xi chromatin structure. reconsti... | 1 |
cyclin-dependent kinase inhibitor 1a (cdkn1a), also known as p21cip1/waf1, is a master downstream effector of tumor suppressors. in this study, we experimentally demonstrate through a high-throughput luciferase reporter screen that p21cip1/waf1 can be directly targeted by nearly 28 micrornas (mirnas). the results were ... | 1 |
microrna-1 (mir-1) is preferentially expressed in cardiac muscles, and the expression has been demonstrated to be involved in cardiac development and cardiovascular diseases. here we report that mir-1 is closely related with ischemia/reperfusion injury in a rat model. the level of mir-1 is inversely correlated with bcl... | 1 |
endothelial cell migration induced in response to vascular endothelial growth factor (vegf) is a crucial step of angiogenesis and it depends on the activation of the p38 map-kinase pathway downstream of vegfr2. in this study, we investigated the role of micrornas (mirnas) in regulating these processes. we found that th... | 1 |
gammaherpesviruses, including the human pathogens epstein-barr virus (ebv) and kaposi's sarcoma-associated herpesvirus (kshv), establish lifelong latent infection in b cells and are associated with a variety of tumors. in addition to protein coding genes, these viruses encode numerous micrornas (mirnas) within their ge... | 1 |
mirnas silence gene expression by repressing translation and/or by promoting mrna decay. in animal cells, degradation of partially complementary mirna targets occurs via deadenylation by the caf1-ccr4-not1 deadenylase complex, followed by decapping and subsequent exonucleolytic digestion. to determine how generally mir... | 1 |
the overexpression of the hmga1 proteins is a feature of human malignant neoplasias and has a causal role in cell transformation. the aim of our study has been to investigate the micrornas (mirnas or mirs) regulated by the hmga1 proteins in the process of cell transformation analyzing the mirna expression profile of v-... | 1 |
hypoxia-induced pulmonary hypertension (ph), which is characterized by vasoconstriction and subsequent structural remodeling of blood vessels, is an important event in chronic obstructive pulmonary disease patients and in people living at high altitudes. hypoxia-inducible factor-1α (hif-1α) and its regulator four-and-a... | 1 |
respiratory syncytial virus (rsv) causes substantial morbidity and life-threatening lower respiratory tract disease in infants, young children and the elderly. understanding the host response to rsv infection is critical for developing disease-intervention approaches. the role of micrornas (mirnas) in post-transcriptio... | 1 |
an internal ribosome entry segment (ires) has been identified in the 5' untranslated region (5' utr) of two members of the myc family of proto-oncogenes, c-myc and n-myc. hence, the synthesis of c-myc and n-myc polypeptides can involve the alternative mechanism of internal initiation. here, we show that the 5' utr of l... | 1 |
single micrornas are usually associated with hundreds of putative target genes that can influence multiple phenotypic traits in drosophila, ranging from development to behaviour. we investigated the function of drosophila mir-210 in circadian behaviour by misexpressing it within circadian clock cells. manipulation of m... | 1 |
background pulmonary hypertension (ph) is a proliferative disorder associated with enhanced proliferation and suppressed apoptosis of pulmonary artery smooth muscle cells (pasmcs). our lately study demonstrated that let-7g inhibited hypoxia-induced proliferation of pasmcs via repressing c-myc-bmi-1-p16 signaling pathwa... | 1 |
many molecular pathways involved in heart disease have their roots in evolutionarily ancient developmental programs that depend critically on gene dosage and timing. micrornas (mirnas) modulate gene dosage posttranscriptionally, and among these, the muscle-specific mir-1 is particularly important for developing and mai... | 1 |
aims atherosclerosis is the most common cause of cardiovascular disease, such as myocardial infarction and stroke. previous study revealed that microrna (mir)-134 promotes lipid accumulation and proinflammatory cytokine secretion through angiopoietin-like 4 (angptl4)/lipid lipoprotein (lpl) signaling in thp-1 macrophag... | 1 |
the mechanisms by which deregulated nuclear factor erythroid-2-related factor 2 (nrf2) and kelch-like ech-associated protein 1 (keap1) signaling promote cellular proliferation and tumorigenesis are poorly understood. using an integrated genomics and ¹³c-based targeted tracer fate association (ttfa) study, we found that... | 1 |
mir-155 acts as an oncogenic mir in b-cell lymphoproliferative disorders, including waldenstrom macroglobulinemia (wm) and chronic lymphocytic leukemia, and is therefore a potential target for therapeutic intervention. however, efficient targeting of mirs in tumor cells in vivo remains a significant challenge for the d... | 1 |
chronic lymphocytic leukemia (cll) is the most common human leukemia and is characterized by predominantly nondividing malignant b cells overexpressing the antiapoptotic b cell lymphoma 2 (bcl2) protein. mir-15a and mir-16-1 are deleted or down-regulated in the majority of clls. here, we demonstrate that mir-15a and mi... | 1 |
the nonselective β-adrenergic receptor antagonist (β-blocker) carvedilol has been shown to protect against myocardial injury, but the detailed underlying mechanisms are unclear. we recently reported that carvedilol stimulates the processing of microrna (mir)-199a-3p and mir-214 in the heart via β-arrestin1-biased β1-ad... | 1 |
nuclear factor of activated t cells (nfat) proteins are ca(2+)-regulated transcription factors that control gene expression in many cell types. nfat proteins are heavily phosphorylated and reside in the cytoplasm of resting cells; when cells are stimulated by a rise in intracellular ca(2+), nfat proteins are dephosphor... | 1 |
micrornas (mirnas) are short noncoding rnas, which post-transcriptionally regulate gene expression. mirnas are transcribed as precursors and matured to active forms by a series of enzymes, including dicer. mirnas are important in governing cell differentiation, development, and disease. we have recently developed a fee... | 1 |
the transcriptional repressor bcl6 is a critical regulator of t helper cell fate, and inhibits th2-type inflammation. we have found that microrna-21 (mir-21) is a novel target gene for bcl6 in treg cells. bcl6 represses and stat3 activates mir-21 transcription through a stat3 binding element in the promoter, indicating... | 1 |
the transcriptional networks that regulate embryonic stem (es) cell pluripotency and lineage specification are the subject of considerable attention. to date such studies have focused almost exclusively on protein-coding transcripts. however, recent transcriptome analyses show that the mammalian genome contains thousan... | 1 |
cooperation between dna, rna and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. here, we report that endoderm differentiation is regulated by the interaction between the l... | 1 |
obesity, type 2 diabetes, and heart failure are associated with aberrant cardiac metabolism. we show that the heart regulates systemic energy homeostasis via med13, a subunit of the mediator complex, which controls transcription by thyroid hormone and other nuclear hormone receptors. med13, in turn, is negatively regul... | 1 |
in caenorhabditis elegans, the heterochronic pathway controls the timing of developmental events during the larval stages. a component of this pathway, the let-7 small regulatory rna, is expressed at the late stages of development and promotes the transition from larval to adult (l/a) stages. the stage-specificity of l... | 1 |
both micrornas and alternative pre-mrna splicing have been implicated in the development of the nervous system (ns), but functional interactions between these two pathways are poorly understood. we demonstrate that the neuron-specific microrna mir-124 directly targets ptbp1 (ptb/hnrnp i) mrna, which encodes a global re... | 1 |
in prokaryotes, small noncoding rnas (snrnas) of 50-500 nt are produced that are important in bacterial virulence and response to environmental stimuli. here, we identified and characterized snrnas from the endosymbiotic bacteria, wolbachia, which are widespread in invertebrates and cause reproductive manipulations. mo... | 1 |
hedgehog (hh) signaling plays many important roles in developmental processes and cancers. smoothened (smo) is an important signal transducer in the hh pathway, and its expression is tightly regulated by several different post-transcriptional mechanisms. however, whether micrornas (mirnas) are involved in smo regulatio... | 1 |
recently, researchers have uncovered the presence of many long noncoding rnas (lncrnas) in embryonic stem cells and believe they are important regulators of the differentiation process. however, there are only a few examples explicitly linking lncrna activity to transcriptional regulation. here, we used transcript coun... | 1 |
once protein-coding, the x-inactivation center (xic) is now dominated by large noncoding rnas (ncrna). x chromosome inactivation (xci) equalizes gene expression between mammalian males and females by inactivating one x in female cells. xci requires xist, an ncrna that coats the x and recruits polycomb proteins. how xis... | 1 |
while recent insights indicate that the transcription factor krüppel-like factor 4 (klf4) is indispensable for vascular homeostasis, its exact role in proliferation and angiogenesis and how it functions remain unresolved. thus, the aim of the present study was to evaluate the role of klf4 in the proliferations of endot... | 1 |
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RNAcentral Litscan ncRNA Related Abstracts
This is a dataset of abstracts that have been labelled relevant to ncRNA or not. Relevant articles have the label 1, irrelevant have the label 0
How was it made
The dataset was built in five parts:
- ncRNA related articles from tarbase
- ncRNA related articles from Rfam
- ncRNA related articles from GO curation
- Manually annotated ncRNA related articles
- Non ncRNA related articles
TarBase
TarBase is a database of miRNAs and their targets. This data is curated from the literature, so by definition, the papers they cite for the interactions are relevant for ncRNA. This is somewhat limited to miRNA though
Rfam
Rfam is the ncRNA families database, and has families for >4000 RNAs. They are mostly miRNAs, but also cover a lot of other types, and the non-miRNA part is expanding. Rfam families are usually built from an alignmentthat is published, so the papers mentioned by Rfam families will be relevant to ncRNA
GO
GO is the Gene Ontology, a knowledge base of function in biology. A subset of annotations in GO are manually curated by human curators reading papers, so those papers curated with ncRNA relevant terms will definitely be relevant to ncRNA. A large fraction of the GO curation is about miRNA-mRNA interactions, but there is a bit of other stuff in there as well; reflecting the type of analyses done in low throughput experiments on ncRNA
Manually annotated articles
A set of ~400 abstracts were manually assessed for relevance to ncRNA by members of the RNAcentral & Rfam teams. These were drawn from a EuropePMC query designed to pull in as many potentially relevant articles as possible. These should cover all RNA types, but the set is relatively small
Non-ncRNA related articles
To provide our negative set, we used this EuropePMC search to retrieve ~3500 articles:
f'/search?query=(IN_EPMC:Y AND OPEN_ACCESS:Y AND NOT SRC:PPR AND NOT "rna" ' \
f'AND NOT "mrna" AND NOT "ncrna" AND NOT "lncrna" AND NOT "rrna" AND NOT "sncrna" AND NOT "mirna") ' \
f'&sort_cited:y&pageSize=500&cursorMark={page}&format=json'
This is the opposite query to the one used in production for LitScan, so should be pulling in totally irrelevant articles.
Limitations
- Most of the positive set come from annotations or other linkages with miRNAs. Therefore, we kind of expect this dataset to produce a model that is good at finding miRNA related articles, but it may struggle when filtering articles relevant for other types (e.g. snoRNA) that are under-represented
- The negative set may be too easy to separate from the positive, since they are deliberately very irrelevant
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