Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis [RIP-seq]
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ABSTRACT:
PROVIDER: PRJNA528028 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8752800_1.fastq.gz | Fastqsanger.gz | |||
| SRR8752800_2.fastq.gz | Fastqsanger.gz | |||
| SRR8752801_1.fastq.gz | Fastqsanger.gz | |||
| SRR8752801_2.fastq.gz | Fastqsanger.gz | |||
| SRR8752802_1.fastq.gz | Fastqsanger.gz |
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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:Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis
| PRJNA528029 | ENA
Project description:Intragenic Heterochromatin-dependent RNA Polyadenylation mediated by a Protein Complex in Arabidopsis [ChIP-seq]
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Project description:Mechanism for full-length RNA processing over intragenic heterochromatin
2014-04-22 | E-MTAB-4475 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-03-14 | GSE128540 | GEO
Project description:Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development. We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full-length OsXRNL and regulate miRNA abundance. We found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development. Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.
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Project description:The translational reactivation of maternal mRNAs encoding the drivers of vertebrate meiosis is accomplished mainly by cytoplasmic polyadenylation. The Cytoplasmic Polyadenylation Elements (CPEs) present in the 3’ UTR of these transcripts, together with their cognate CPE-binding proteins (CPEBs), define a combinatorial code that determines the timing and extent of translational activation upon meiosis resumption. In addition, the RNA-binding protein Musashi1 (Msi1) regulates the polyadenylation of CPE-containing mRNAs by an as yet undefined CPEB-dependent or -independent mechanism. Here we show that Msi1 alone does not support cytoplasmic polyadenylation, but its binding triggers the remodeling of RNA structure, thereby exposing adjacent CPEs and stimulating polyadenylation. Thus, Msi1 directs the preferential use of specific CPEs, which in turn affects the timing and extent of polyadenylation during meiotic progression. Genome-wide analysis of CPEB1- and Msi-associated mRNAs identified 491 common targets, thus revealing a new layer of CPE-mediated translational control.
2017-07-17 | GSE68098 | GEO
Project description:The translational reactivation of maternal mRNAs encoding the drivers of vertebrate meiosis is accomplished mainly by cytoplasmic polyadenylation. The Cytoplasmic Polyadenylation Elements (CPEs) present in the 3’ UTR of these transcripts, together with their cognate CPE-binding proteins (CPEBs), define a combinatorial code that determines the timing and extent of translational activation upon meiosis resumption. In addition, the RNA-binding protein Musashi1 (Msi1) regulates the polyadenylation of CPE-containing mRNAs by an as yet undefined CPEB-dependent or -independent mechanism. Here we show that Msi1 alone does not support cytoplasmic polyadenylation, but its binding triggers the remodeling of RNA structure, thereby exposing adjacent CPEs and stimulating polyadenylation. Thus, Msi1 directs the preferential use of specific CPEs, which in turn affects the timing and extent of polyadenylation during meiotic progression. Genome-wide analysis of CPEB1- and Msi-associated mRNAs identified 491 common targets, thus revealing a new layer of CPE-mediated translational control.
2017-07-17 | GSE68097 | GEO
Project description:The translational reactivation of maternal mRNAs encoding the drivers of vertebrate meiosis is accomplished mainly by cytoplasmic polyadenylation. The Cytoplasmic Polyadenylation Elements (CPEs) present in the 3’ UTR of these transcripts, together with their cognate CPE-binding proteins (CPEBs), define a combinatorial code that determines the timing and extent of translational activation upon meiosis resumption. In addition, the RNA-binding protein Musashi1 (Msi1) regulates the polyadenylation of CPE-containing mRNAs by an as yet undefined CPEB-dependent or -independent mechanism. Here we show that Msi1 alone does not support cytoplasmic polyadenylation, but its binding triggers the remodeling of RNA structure, thereby exposing adjacent CPEs and stimulating polyadenylation. Thus, Msi1 directs the preferential use of specific CPEs, which in turn affects the timing and extent of polyadenylation during meiotic progression. Genome-wide analysis of CPEB1- and Msi-associated mRNAs identified 491 common targets, thus revealing a new layer of CPE-mediated translational control.
2017-07-17 | GSE68095 | GEO