RNA-binding protein crosstalks
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28432 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2767190_1.fastq.gz | Fastqsanger.gz | |||
| ERR2767190_2.fastq.gz | Fastqsanger.gz | |||
| ERR2767185_1.fastq.gz | Fastqsanger.gz | |||
| ERR2767185_2.fastq.gz | Fastqsanger.gz | |||
| ERR2767186_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
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Project description:In eukaryotic cells, the constitutive heterochromatins, characterized by enrichments of DNA cytosine methylation and repressive histone modifications, are formed in both intergenic regions and gene body regions. The ASI1-AIPP1-EDM2 (AAE) complex has been shown to participates in the RNA polyadenylation (poly A) regulation of intronic heterochromatin-containing genes. While, how AAE complex components coordinately interacts with the chromatin and RNA remains largely unknown. Here, based on multi-omics analysis, we proved that ASI1 and EDM2 mostly target the common genomic regions and display high preference to intragenic heterochromatin within the transposable element (TE)-overlapping genes. Besides interplay with chromatin, ASI1 also displays high binding affinity to RNA transcripts from intragenic heterochromatin regions. Evidence from poly (A)-specific sequencing proved that AAE complex controls the choice of poly (A) sites not only in genes with intronic heterochromatin but also in heterochromatic TE-overlapping genes. Importantly, we revealed that AAE complex also participates in the alternative splicing of TE-overlapping gene RPP4. Moreover, evidences from gene expression and poly (A) sequencing revealed that RRM protein FPA functions antagonistically with AAE complex to control polyadenylation of histone demethylase gene IBM1 in locus-dependent manner. Taken together, our results provide fundamental evidences that AAE complex interacts with both the chromatin and RNA in the intragenic heterochromatin to regulate poly (A) site choice, and a bidirectional regulation mechanism of intragenic heterochromatin-dependent RNA processing exists in Arabidopsis. Our finding gained further insights into the molecular interaction pattern of AAE complex with targets and will help to better understand the complicated interplay between epigenetic modification-shaped chromatin and RNA processing.
2022-03-14 | GSE128501 | GEO
Project description:In eukaryotic cells, the constitutive heterochromatins, characterized by enrichments of DNA cytosine methylation and repressive histone modifications, are formed in both intergenic regions and gene body regions. The ASI1-AIPP1-EDM2 (AAE) complex has been shown to participates in the RNA polyadenylation (poly A) regulation of intronic heterochromatin-containing genes. While, how AAE complex components coordinately interacts with the chromatin and RNA remains largely unknown. Here, based on multi-omics analysis, we proved that ASI1 and EDM2 mostly target the common genomic regions and display high preference to intragenic heterochromatin within the transposable element (TE)-overlapping genes. Besides interplay with chromatin, ASI1 also displays high binding affinity to RNA transcripts from intragenic heterochromatin regions. Evidence from poly (A)-specific sequencing proved that AAE complex controls the choice of poly (A) sites not only in genes with intronic heterochromatin but also in heterochromatic TE-overlapping genes. Importantly, we revealed that AAE complex also participates in the alternative splicing of TE-overlapping gene RPP4. Moreover, evidences from gene expression and poly (A) sequencing revealed that RRM protein FPA functions antagonistically with AAE complex to control polyadenylation of histone demethylase gene IBM1 in locus-dependent manner. Taken together, our results provide fundamental evidences that AAE complex interacts with both the chromatin and RNA in the intragenic heterochromatin to regulate poly (A) site choice, and a bidirectional regulation mechanism of intragenic heterochromatin-dependent RNA processing exists in Arabidopsis. Our finding gained further insights into the molecular interaction pattern of AAE complex with targets and will help to better understand the complicated interplay between epigenetic modification-shaped chromatin and RNA processing.
2022-03-14 | GSE128484 | GEO
Project description:In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
2018-07-03 | GSE114536 | GEO
Project description:In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
2018-07-03 | GSE114538 | GEO
Project description:In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
2018-07-03 | GSE114537 | GEO
Project description:In S. pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNAPII-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
2018-07-03 | GSE114535 | GEO
Project description:KSRP is involved in RNA processing at multiple levels including alternative splicing, mRNA stability, mRNA localization and translation efficiency. Dysregulation KSRP can cause to hematological malignancies. However, the direct contribution of KSRP to myeloid lineage differentiation is poorly understood. KSRP, as a KH-type splicing regulatory protein, which interacts with single-stand AU-rich element containing mRNA and mediated mRNA decay, also serves as a component of Drosha and Dicer complexes and regulates the biogenesis of miRNAs. Whether KSRP mediated miRNAs maturation participated in myeloid lineage differentiation is unknown. Here, we analysis the miRNAs processing during over-expression KSRP in THP-1 cells by poly-A(riched) RNA-seq and miRNA-Seq. Our results suggest that KSRP regulate a class of miRNAs maturation and have a critical function in myeloid lineage differentiation.
2017-08-01 | GSE87318 | GEO
Project description:In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis. Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein. The complex also may contain the Pol II CTD phosphatase CPL2, the plant homeodomain-containing protein AIPP2, and another BAH domain protein, AIPP3. As is the case with dysfunction of ASI1 and EDM2, dysfunction of AIPP1 impedes the use of distal polyadenylation sites at tested intronic HC-containing genes, such as the histone demethylase gene IBM1, resulting in a lack of functional full-length transcripts. A mutation in AIPP1 causes silencing of the 35S-SUC2 transgene and genome-wide CHG hypermethylation at gene body regions, consistent with the lack of full-length functional IBM1 transcripts in the mutant. Interestingly, compared with asi1, edm2, and aipp1 mutations, mutations in CPL2, AIPP2, and AIPP3 cause the opposite effects on the expression of intronic HC-containing genes and other genes, suggesting that CPL2, AIPP2, and AIPP3 may form a distinct subcomplex. These results advance our understanding of the interplay between heterochromatic epigenetic modifications and RNA processing in higher eukaryotes.
2017-08-17 | GSE98655 | GEO
Project description:RNA-binding proteins coordinate the fates of multiple RNAs, but the principles underlying these global interactions remain poorly understood. We elucidated regulatory mechanisms of the RNA-binding protein HuR, by integrating data from diverse high-throughput targeting technologies, specifically PAR-CLIP, RIP-chip, and whole-transcript expression profiling. The number of binding sites per transcript, degree of HuR-association, and degree of HuR-dependent RNA stabilization were positively correlated. Pre-mRNA and mature mRNA containing both intronic and 3' UTR binding sites were more highly stabilized than transcripts with only 3' UTR or only intronic binding sites, suggesting that HuR couples pre-mRNA processing with mature mRNA stability. We also observed HuR-dependent splicing changes and substantial binding of HuR in poly-pyrimidine tracts of pre-mRNAs. Comparison of the spatial patterns surrounding HuR and miRNA binding sites provided functional evidence for HuR-dependent antagonism of proximal miRNA-mediated repression. We conclude that HuR coordinates gene expression outcomes at multiple interconnected steps of RNA processing.
2011-08-19 | GSE29779 | GEO
Project description:RNA-binding proteins coordinate the fates of multiple RNAs, but the principles underlying these global interactions remain poorly understood. We elucidated regulatory mechanisms of the RNA-binding protein HuR, by integrating data from diverse high-throughput targeting technologies, specifically PAR-CLIP, RIP-chip, and whole-transcript expression profiling. The number of binding sites per transcript, degree of HuR-association, and degree of HuR-dependent RNA stabilization were positively correlated. Pre-mRNA and mature mRNA containing both intronic and 3' UTR binding sites were more highly stabilized than transcripts with only 3' UTR or only intronic binding sites, suggesting that HuR couples pre-mRNA processing with mature mRNA stability. We also observed HuR-dependent splicing changes and substantial binding of HuR in poly-pyrimidine tracts of pre-mRNAs. Comparison of the spatial patterns surrounding HuR and miRNA binding sites provided functional evidence for HuR-dependent antagonism of proximal miRNA-mediated repression. We conclude that HuR coordinates gene expression outcomes at multiple interconnected steps of RNA processing. HuR (ELAVL1) PAR-CLIP
2011-08-19 | E-GEOD-29779 | biostudies-arrayexpress