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Series GSE188412 Query DataSets for GSE188412
Status Public on Nov 06, 2024
Title The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag]
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin places fundamental physical constraints on transcription (Gamarra and Narlikar, 2021). The PAF1 complex (PAF1C), a hexamer of PAF1, LEO1, CTR9, SKI8, CDC73 and RTF1, plays a critical role in transcription with incompletely understood mechanisms. During transcriptional elongation, PAF1C is one of the positive elongation factors in complex with RNA polymerase II (Pol II) to facilitate elongation through chromatin (Vos et al., 2018), but it is unclear yet if negative elongation factors are needed concurrently to restrain elongation. Here we show that besides decreasing elongation rate, LEO1 knockout in human K562 cells increases transcriptional readthrough and cellular level of C-terminal domain (CTD) phosphorylated Pol II while increases and decreases transcriptional output of several hundred genes, respectively. Mechanistic analyses taking proteomic, functional genomic and biochemical approaches discovered that PAF1C regulates transcriptional termination in part through recruiting PNUTS-PP1γ complex and facilitates Pol II transcriptional re-initiation through recruiting TOX4-PP1α complex. Moreover, Paf1 conditional knockout in mice severely blocks T cell development, increases cellular level of CTD phosphorylated Pol II, mainly decreases Pol II occupancy and transcriptional output in double positive T cells, and importantly, the regulation of re-initiation by PAF1C through TOX4-PP1α complex is conserved between mouse and human. Our results also suggest that PNUTS-PP1γ and TOX4-PP1α bind PAF1C to restrain Pol II elongation through chromatin. These findings not only establish PAF1C as a critical regulator of transcriptional termination and re-initiation besides elongation but also advanced current understanding of elongation.
 
Overall design CUT&Tag of proteins envolved in transcription regulation in control , LEO1 KO and PNUTS KO human K562 cells and in WT and Paf1 cKO DP thymocytes
 
Contributor(s) Yu M, Liu Z, Wu A, Wang T
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 08, 2021
Last update date Nov 06, 2024
Contact name Aiwei Wu
E-mail(s) aiwei.wu@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Department School of Life Sciences and Biotechnology
Lab Ming Yu
Street address 800 Dongchuan Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200240
Country China
 
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (71)
GSM5680964 control for PAF1 data Pol II CUT&Tag rep1
GSM5680965 control for PAF1 data Pol II CUT&Tag rep2
GSM5680966 LEO1 KO Pol II CUT&Tag rep1
This SubSeries is part of SuperSeries:
GSE188417 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation
Relations
BioProject PRJNA778758
SRA SRP345062

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
GSE188412_Ctrl.CSTF64.CUTTag.bw 48.8 Mb (ftp)(http) BW
GSE188412_Ctrl.NELFE.CUTTag.bw 56.0 Mb (ftp)(http) BW
GSE188412_Ctrl.PNUTS.CUTTag.bw 29.6 Mb (ftp)(http) BW
GSE188412_Ctrl.TOX4.CUTTag.bw 41.0 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_KO.PPP1CC.CUTTag.bw 47.5 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_KO.PolII.CUTTag.bw 60.5 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_KO.SPT5.CUTTag.bw 59.7 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_KO.ser2p.CUTTag.bw 58.9 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_KO.ser5p.CUTTag.bw 50.7 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_rescue.LEO1.CUTTag.bw 63.3 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_rescue.PNUTS.CUTTag.bw 37.7 Mb (ftp)(http) BW
GSE188412_Ctrl_for_LEO1_rescue.ser2p.CUTTag.bw 63.5 Mb (ftp)(http) BW
GSE188412_Ctrl_for_PNUTS_KO.PolII.CUTTag.bw 64.1 Mb (ftp)(http) BW
GSE188412_Ctrl_for_PNUTS_KO.ser2p.CUTTag.bw 53.7 Mb (ftp)(http) BW
GSE188412_Ctrl_for_PNUTS_KO.ser5p.CUTTag.bw 48.5 Mb (ftp)(http) BW
GSE188412_LEO1_KO.CSTF64.CUTTag.bw 57.8 Mb (ftp)(http) BW
GSE188412_LEO1_KO.NELFE.CUTTag.bw 52.5 Mb (ftp)(http) BW
GSE188412_LEO1_KO.PNUTS.CUTTag.bw 26.5 Mb (ftp)(http) BW
GSE188412_LEO1_KO.PPP1CC.CUTTag.bw 36.7 Mb (ftp)(http) BW
GSE188412_LEO1_KO.PolII.CUTTag.bw 61.2 Mb (ftp)(http) BW
GSE188412_LEO1_KO.SPT5.CUTTag.bw 64.1 Mb (ftp)(http) BW
GSE188412_LEO1_KO.TOX4.CUTTag.bw 37.8 Mb (ftp)(http) BW
GSE188412_LEO1_KO.ser2p.CUTTag.bw 65.7 Mb (ftp)(http) BW
GSE188412_LEO1_KO.ser5p.CUTTag.bw 48.8 Mb (ftp)(http) BW
GSE188412_LEO1_KO_for_LEO1_rescue.LEO1.CUTTag.bw 48.6 Mb (ftp)(http) BW
GSE188412_LEO1_KO_for_LEO1_rescue.PNUTS.CUTTag.bw 33.2 Mb (ftp)(http) BW
GSE188412_LEO1_KO_for_LEO1_rescue.ser2p.CUTTag.bw 60.8 Mb (ftp)(http) BW
GSE188412_LEO1_WT2_for_LEO1_rescue.LEO1.CUTTag.bw 63.3 Mb (ftp)(http) BW
GSE188412_LEO1_WT2_for_LEO1_rescue.PNUTS.CUTTag.bw 36.8 Mb (ftp)(http) BW
GSE188412_LEO1_WT2_for_LEO1_rescue.ser2p.CUTTag.bw 70.1 Mb (ftp)(http) BW
GSE188412_PNUTS_KO.PolII.CUTTag.bw 62.9 Mb (ftp)(http) BW
GSE188412_PNUTS_KO.ser2p.CUTTag.bw 59.2 Mb (ftp)(http) BW
GSE188412_PNUTS_KO.ser5p.CUTTag.bw 44.2 Mb (ftp)(http) BW
GSE188412_Paf1_WT.PolII.CUTTag.bw 78.3 Mb (ftp)(http) BW
GSE188412_Paf1_WT.ser2p.CUTTag.bw 76.4 Mb (ftp)(http) BW
GSE188412_Paf1_cKO.PolII.CUTTag.bw 87.6 Mb (ftp)(http) BW
GSE188412_Paf1_cKO.ser2p.CUTTag.bw 65.2 Mb (ftp)(http) BW
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