Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA336102 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes
| PRJNA336107 | ENA
Project description:Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq PROLIF-SEN]
| PRJNA336104 | ENA
Project description:Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq siRNA H2A.Z]
| PRJNA336105 | ENA
Project description:Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are generally produced from specific promoters. By genome-wide approaches and in depth analyses at specific loci in human cells undergoing senescence, we uncover a family of antisense RNAs produced by transcriptional read-through at convergent protein-coding genes. Importantly, these antisense RNAs, that we named STARTs, repress the expression of their corresponding sense RNAs. We found that the elongation rate of RNA pol II is limited downstream of the TTS at START loci in proliferative cells. This allows transcription termination to occur before the RNA pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes. In proliferative cells, STARTs are repressed by the histone variant H2A.Z, whose local occupancy decreases in senescence. Our results thus uncover a novel mechanism of gene expression regulation, relying on the control of the expression of read-through antisense transcripts at convergent genes and underline the functional importance of the epigenetic control of RNA pol II elongation rate at intergenic regions.
2017-11-28 | GSE85083 | GEO
Project description:Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are generally produced from specific promoters. By genome-wide approaches and in depth analyses at specific loci in human cells undergoing senescence, we uncover a family of antisense RNAs produced by transcriptional read-through at convergent protein-coding genes. Importantly, these antisense RNAs, that we named STARTs, repress the expression of their corresponding sense RNAs. We found that the elongation rate of RNA pol II is limited downstream of the TTS at START loci in proliferative cells. This allows transcription termination to occur before the RNA pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes. In proliferative cells, STARTs are repressed by the histone variant H2A.Z, whose local occupancy decreases in senescence. Our results thus uncover a novel mechanism of gene expression regulation, relying on the control of the expression of read-through antisense transcripts at convergent genes and underline the functional importance of the epigenetic control of RNA pol II elongation rate at intergenic regions.
2017-11-28 | GSE85082 | GEO
Project description:Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are generally produced from specific promoters. By genome-wide approaches and in depth analyses at specific loci in human cells undergoing senescence, we uncover a family of antisense RNAs produced by transcriptional read-through at convergent protein-coding genes. Importantly, these antisense RNAs, that we named STARTs, repress the expression of their corresponding sense RNAs. We found that the elongation rate of RNA pol II is limited downstream of the TTS at START loci in proliferative cells. This allows transcription termination to occur before the RNA pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes. In proliferative cells, STARTs are repressed by the histone variant H2A.Z, whose local occupancy decreases in senescence. Our results thus uncover a novel mechanism of gene expression regulation, relying on the control of the expression of read-through antisense transcripts at convergent genes and underline the functional importance of the epigenetic control of RNA pol II elongation rate at intergenic regions.
2017-11-28 | GSE85081 | GEO
Project description:Interventions: Case series:None
Primary outcome(s): exon genes;transcriptional expression;proteome;protein phosphorylation group
Study Design: Sequential
| 2739647 | ecrin-mdr-crc
Project description:The so-called allosteric and torpedo models have been used for the past thirty years to explain how transcription terminates on protein-coding genes. The former invokes conformational changes in the transcription complex and the latter involves degradation of the downstream product of poly(A) signal (PAS) processing. Here, we describe a single mechanism incorporating features of both models. We show that CPSF73 is indispensable for transcriptional termination on protein-coding and its loss causes profound read-through genome-wide. CPSF73 functions upstream of allosteric modifications to the elongation complex that cause Pol II to slow down after the PAS. This state is enriched by rapid depletion of XRN2 and promoted by protein phosphatase 1 (PP1), the inhibition of which confers runaway read-through in the absence of XRN2. These allosteric changes facilitate XRN2-dependent termination, by aiding its capture of Pol II, rather than constituting a termination pathway in themselves. Our experiments unify the long-standing allosteric and torpedo models for transcriptional termination.
2020-01-21 | GSE137727 | GEO
Project description:In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A) fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as 17 polycistronic and complex transcripts. This work also led us to identify many transcript isoforms, including 13 splice and 68 length variants, as well as several transcriptional overlaps. Additionally, we determined previously unascertained transcriptional start and polyadenylation sites. We analyzed the transcriptional activity from the complementary DNA strand in five convergent HSV gene pairs with quantitative RT-PCR and detected antisense RNAs in each gene. This part of the study revealed an inverse correlation between the expressions of convergent partners. Our work adds new insights for understanding the complexity of the pervasive transcriptional overlaps by suggesting that there is a crosstalk between adjacent and distal genes through interaction between their transcription apparatuses. We also identified transcripts overlapping the HSV replication origins, which may indicate an interplay between the transcription and replication machineries. The relative abundance of HSV-1 transcripts has also been established by using a novel method based on the calculation of sequencing reads for the analysis.
2017-07-12 | GSE97785 | GEO
Project description:Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
| PRJNA488719 | ENA