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Series GSE140930 Query DataSets for GSE140930
Status Public on Jan 15, 2021
Title A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. Through proteomics screens, we find that the TCR-specific CSB protein loads the evolutionary conserved PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. PAF1C is dispensable for TCR-mediated repair, but is essential for recovery of RNA synthesis after UV irradiation, suggesting an uncoupling between DNA repair and transcription recovery. Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.
Overall design BrU-seq and ChIP-seq in human cell lines either untreated (mock) or 3h, 8h or 26h after UV-C treatment with varying dose (as indicated per sample). ChIP-seq was performed targeting RPB1 or PAF1 in either WT or CSB knockout U2OS cells or in U2OS cells in which PAF1 was depleted using the auxin-inducible degron system. BrU-seq was also performed on U2OS cells with and without auxin-induced depletion of PAF1.
Contributor(s) van den Heuvel D, Luijsterburg MS
Citation(s) 33637760
Submission date Nov 25, 2019
Last update date Apr 16, 2021
Contact name Martijn S. Luijsterburg
Organization name LUMC
Department Human Genetics
Lab Luijsterburglab
Street address Einthovenweg 20
City Leiden
State/province zuid-holland
ZIP/Postal code 2333ZC
Country Netherlands
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (79)
GSM4190576 data_Input_Total (CSB-KO 6J8h)
GSM4190577 data_Input2_Total (CSB-KO noUV)
GSM4190578 data_Input3_Total (WT 6J8h)
BioProject PRJNA591582
SRA SRP233175

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140930_BrUseq_Average.xlsx 320.1 Kb (ftp)(http) XLSX
GSE140930_RNAPII_TravelingRatio_Top3000.txt.gz 677.3 Kb (ftp)(http) TXT
GSE140930_UbH2B_Distribution_Above100kbGenes_averages.xlsx 455.8 Kb (ftp)(http) XLSX
GSE140930_averages_Normalized_750TSS3000_Top3000.txt.gz 63.4 Kb (ftp)(http) TXT
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