Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE80046 | GEO | 2016/11/09
SECONDARY ACCESSION(S): PRJNA318241
REPOSITORIES: GEO
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Project description:While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters. Surprisingly, we find that H3K9me3-a histone modification typically associated with transcriptional repression-is more enriched at the promoters of active lincRNA loci than at those of active mRNAs. Moreover, H3K9me3-marked lincRNA genes are more tissue-specific. The most discriminant differences between lincRNAs and mRNAs involve splicing. LincRNAs are less efficiently spliced, which cannot be explained by differences in U1 binding or the density of exonic splicing enhancers but may be partially attributed to lower U2AF65 binding and weaker splicing-related motifs. Conversely, the stability of lincRNAs and mRNAs is similar, differing only with regard to the location of stabilizing protein binding sites. Finally, we find that certain transcriptional properties are correlated with higher evolutionary conservation in both DNA and RNA motifs and are enriched in lincRNAs that have been functionally characterized.
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Project description:While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. Surprisingly, we find that H3K9me3 –typically associated with transcriptional repression–is enriched at active lncRNA loci. However, the most discriminant differences between lncRNAs and mRNAs involve splicing: only half of lncRNAs are efficiently spliced, which can be partially attributed to defects in lncRNA splicing signals and diminished U2AF65 binding. These attributes are conserved between humans and mice. Finally, we find that certain transcriptional properties are enriched in known, functionally characterized lncRNAs, demonstrating that our multidimensional analysis might discern lncRNAs that are likely to be functional
2016-11-09 | GSE80045 | GEO
Project description:While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. Surprisingly, we find that H3K9me3 –typically associated with transcriptional repression–is enriched at active lncRNA loci. However, the most discriminant differences between lncRNAs and mRNAs involve splicing: only half of lncRNAs are efficiently spliced, which can be partially attributed to defects in lncRNA splicing signals and diminished U2AF65 binding. These attributes are conserved between humans and mice. Finally, we find that certain transcriptional properties are enriched in known, functionally characterized lncRNAs, demonstrating that our multidimensional analysis might discern lncRNAs that are likely to be functional
2016-11-09 | GSE80043 | GEO
Project description:Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs
| PRJNA318241 | ENA
Project description:During meiosis in yeast, global splicing efficiency increases and then decreases. Here we provide evidence that splicing improves due to reduced competition for the splicing machinery. The timing of this regulation corresponds to repression and reactivation of ribosomal protein genes (RPGs) during meiosis. In vegetative cells, RPG repression by rapamycin treatment also increases splicing efficiency. Downregulation of the RPG-dedicated transcription factor gene IFH1 genetically suppresses two spliceosome mutations, prp11-1 and prp4-1, and globally restores splicing efficiency in prp4-1 cells. We conclude that the splicing apparatus is limiting and that pre-messenger RNAs compete. Splicing efficiency of a pre-mRNA therefore depends not just on its own concentration and affinity for limiting splicing factor(s), but also on those of competing pre-mRNAs. Competition between RNAs for limiting processing factors appears to be a general condition in eukaryotes for a variety of posttranscriptional control mechanisms including microRNA (miRNA) repression, polyadenylation, and splicing.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2021-07-14 | GSE158599 | GEO
Project description:BACKGROUND:Competitive endogenous RNAs (ceRNAs) have revealed a new mechanism of interaction between RNAs. However, an understanding of the ceRNA regulatory network in Wilms tumour (WT) remains limited. METHODS:The expression profiles of mRNAs, miRNAs and lncRNAs in Wilms tumour samples and normal samples were obtained from the Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database. The EdgeR package was employed to identify differentially expressed lncRNAs, miRNAs and mRNAs. Functional enrichment analyses via the ClusterProfile R package were performed, and the lncRNA-miRNA-mRNA interaction ceRNA network was established in Cytoscape. Subsequently, the correlation between the ceRNA network and overall survival was analysed. RESULTS:A total of 2037 lncRNAs, 154 miRNAs and 3609 mRNAs were identified as differentially expressed RNAs in Wilms tumour. Of those, 205 lncRNAs, 26 miRNAs and 143 mRNAs were included in the ceRNA regulatory network. The results of Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in terms related to response to mechanical stimuli, transcription factor complexes, and transcription factor activity (related to RNA polymerase II proximal promoter sequence-specific DNA binding). The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were mainly enriched in pathways related to the cell cycle. The survival analysis results showed that 16 out of the 205 lncRNAs, 1 out of 26 miRNAs and 5 out of 143 mRNAs were associated with overall survival in Wilms tumour patients (P?<?0.05). CONCLUSIONS:CeRNA networks play an important role in Wilms tumour. This finding might provide effective, novel insights for further understanding the mechanisms underlying Wilms tumour.
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Project description:Long non-coding RNAs (lncRNAs) can regulate lipid metabolism and adipogenesis. However, there is little research on the role of lncRNAs in fat deposition in pig. In this study, RNA-seq technology was used to analyze the gene expression profiles of subcutaneous adipose tissue in Laiwu (LW) and Large White (LY) pigs. Then, key lncRNAs and genes associated with lipid metabolism and adipogenic differentiation were identified. Fifty four lncRNAs and 482 known mRNAs were differentially expressed in the two pig breeds. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that differentially expressed genes and the target genes of differentially expressed lncRNAs were significantly enriched in PPAR signaling pathway and biological processes including fat cell differentiation and fatty acid metabolism. Key lncRNAs might regulate adipogenic differentiation and fatty acid metabolism by regulating genes involved in above signaling pathway and biological processes. Specifically, XLOC_014379, XLOC_011279, XLOC_064871, XLOC_019518 and XLOC_013639 might target SCD, LPIN1, TRIB3, EGR2 and FABP3, respectively, and then play critical regulatory role. These results are useful for understanding fat deposition in pig, breeding livestock with high quality meat, and preventing and treating lipid metabolic disease.
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Project description:Follicular development and maturation has a significant impact on goat reproductive performance, and it is therefore important to understand the molecular basis of this process. The importance of long non-coding RNAs (lncRNAs) in mammalian reproduction has been established, but little is known about the roles of lncRNAs in different follicular stages, especially in goats. In this study, RNA sequencing (RNA-seq) of large follicles (>10 mm) and small follicles (<3 mm) of Chuanzhong black goats was performed to investigate the regulatory mechanisms of lncRNAs and mRNAs in follicular development and maturation. A total of 8 differentially expressed lncRNAs (DElncRNAs) and 1,799 DEmRNAs were identified, and the majority of these were upregulated in small follicles. MRO, TC2N, CDO1, and NTRK1 were potentially associated with follicular maturation. KEGG pathway analysis showed that the DEmRNAs involved in ovarian steroidogenesis (BMP6, CYP11A1, CYP19A1, 3BHSD, STAR, LHCGR, and CYP51A1) and cAMP signaling play roles in regulating follicular maturation and developmental inhibition respectively. Five target pairs of DElncRNA-DEmRNA, namely, ENSCHIT00000001255-OTX2, ENSCHIT00000006005-PEG3, ENSCHIT00000009455-PIWIL3, ENSCHIT00000007977-POMP, and ENSCHIT00000000834-ACTR3 in co-expression analysis provide a clue in follicular development and maturation of lncRNA-mRNA interaction. Our findings provide a valuable resource for lncRNA studies, and could potentially provide a deeper understanding of the genetic basis and molecular mechanisms of goat follicular development and maturation.
| S-EPMC7773919 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-02-12 | E-GEOD-61236 | biostudies-arrayexpress