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| Status |
Public on Feb 08, 2019 |
| Title |
RNA-binding protein WDR43 binds prevalently to open chromatin and promotes gene transcription |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The intricate regulation of transcription underlies cellular differentiation and development. However, the general relevance of RNA-binding proteins (RBPs) in polymerase (Pol) II transcription is less understood. Here we revealed that WDR43, a novel chromatin-bound RBP, promotes transcription and is essential for self-renewal of embryonic stem cells (ESCs) and early embryonic development. WDR43 binds to promoter-associated non-coding and nascent RNAs, localizes at thousands of gene promoters and enhancers, and interacts with the Pol II transcription machinery. Recombinant WDR43 directly promotes transcription and the release of elongation factor P-TEFb in vitro. Depletion of WDR43 in ESCs leads to global defects in Pol II pause release and mRNA expression. These results demonstrate that WDR43 maintains high-level expression of pluripotency programs by modulating Pol II activity and transcription elongation. To extend these findings, we demonstrated widespread co-occupancy of open chromatin by multiple RBPs, suggesting an unforeseen role for RBPs in transcription control
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| Overall design |
Expression profiling by high throughput sequencing and genome occupancy profiling by high throughput sequencing. chrTAP-seq for WDR43.
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| Contributor(s) |
Bi X, Xu Y, Li T, Li X, LI W, Wang K, Zhan G, Wu Z, Yin Y, Shao W, Lu JY, Wang L, Zhao J, Wu J, Na J, Li G, Li P, Shen X |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 08, 2018 |
| Last update date |
Dec 26, 2020 |
| Contact name |
jinlong lu |
| E-mail(s) |
bioyuyang@hotmail.com
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| Phone |
5853098469
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| Organization name |
University of Rochester
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| Lab |
Gorbunova & Seluanov Labs
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| Street address |
213 Hutchinson Hall
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14627 |
| Country |
USA |
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| Platforms (2) |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA433525 |
| SRA |
SRP132494 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110358_ActD_WDR43-FLAG-ChIP-seq_peaks.bed.gz |
6.1 Kb |
(ftp)(http) |
BED |
| GSE110358_DMSO_WDR43-FLAG-ChIP-seq_peaks.bed.gz |
430.2 Kb |
(ftp)(http) |
BED |
| GSE110358_DRB_WDR43-FLAG-ChIP-seq_peaks.bed.gz |
61.7 Kb |
(ftp)(http) |
BED |
| GSE110358_Pol_II_Ser5P_ChIP-seq-shCtl-1_peaks.bed.gz |
27.8 Kb |
(ftp)(http) |
BED |
| GSE110358_Pol_II_Ser5P_ChIP-seq-shCtl-2_peaks.bed.gz |
37.1 Kb |
(ftp)(http) |
BED |
| GSE110358_Pol_II_Ser5P_ChIP-seq-shWDR43-1_peaks.bed.gz |
95.2 Kb |
(ftp)(http) |
BED |
| GSE110358_Pol_II_Ser5P_ChIP-seq-shWDR43-2_peaks.bed.gz |
110.5 Kb |
(ftp)(http) |
BED |
| GSE110358_RAW.tar |
829.3 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
| GSE110358_Spike-in_RNA-seq_profiling_of_WDR43-depleted_ESCs..txt.gz |
986.3 Kb |
(ftp)(http) |
TXT |
| GSE110358_WDR43_chrTAP_replicate1.tag.negative.strand.bedgraph.gz |
1.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE110358_WDR43_chrTAP_replicate1.tag.positive.strand.bedgraph.gz |
1.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE110358_shCtl-1_Pol_II-hypoP-8WG16_peaks.bed.gz |
291.0 Kb |
(ftp)(http) |
BED |
| GSE110358_shCtl-2_Pol_II-hypoP-8WG16_peaks.bed.gz |
291.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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