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| Status |
Public on Jun 27, 2019 |
| Title |
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.
As part of the ENCODE consortium, we embarked on a large-scale RBP ChIP-seq analysis, revealing broad presence of RBPs in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show great preference for hotspots in the genome, particularly gene promoters, where their binding is frequently linked to transcriptional output. Self-organizing map reveals extensive co-binding events between TFs and RBPs, as exemplified by those between YY1, a known RNA-dependent TF, and RBM25, an RBP involved in alternative splicing. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may bridge specific TF-RNA interactions to control transcription.
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| Overall design |
Examination of RBP-dependent transcription regulation by GRO-seq with 2 replicated experiments in HepG2 cells
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| Contributor(s) |
Xiao R, Chen J, Fu X |
| Citation(s) |
31251911 |
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| Submission date |
Sep 18, 2018 |
| Last update date |
Sep 26, 2019 |
| Contact name |
Rui Xiao |
| E-mail(s) |
xiaorui9@whu.edu.cn
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| Organization name |
Wuhan University
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| Department |
Medical Research Institute
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| Lab |
RNA Biology Lab
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| Street address |
Medical Research Institute, Wuhan University
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430071 |
| Country |
China |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (38)
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| This SubSeries is part of SuperSeries: |
| GSE120110 |
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription |
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| Relations |
| BioProject |
PRJNA491665 |
| SRA |
SRP162015 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE120105_RAW.tar |
2.0 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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