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Series GSE160959 Query DataSets for GSE160959
Status Public on Jan 07, 2022
Title The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In pluripotent cells, a delicate activation-repression balance maintains pro-differentiation genes ready for rapid transcription. The identity of transcription factors (TFs) that specifically repress pro-differentiation genes remains obscure. By targeting ~1,700 TFs with CRISPR loss-of-function perturbations, we found that ZBTB11 and ZFP131 are required to maintain pluripotency in mouse embryonic stem cells (ESCs). ZBTB11 and ZFP131 bind to pro-differentiation genes along with RNA Polymerase II and pausing factor NELF, but without Polycomb repression. Loss of ZBTB11 or ZFP131 leads to a decrease in NELF association, an increase in H3K4me3, transcriptional upregulation of genes associated with three germ layers, and concomitant ESC differentiation. Together, our results suggest ZBTB11 and ZFP131 maintain pluripotency by pausing pro-differentiation genes transcription and present a generalizable framework to maintain cellular potency.
 
Overall design Bulk RNA-seq was used to characterize gene expression in Wildtype, Zbtb10KO, Zbtb11KO, and Zfp131KO cells grown in the presence of +2i+LIF or -2i+LIF.
 
Contributor(s) Garipler G, Lu C, Morrisey A, Lopez-Zepeda LS, Vidal SE, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO
Citation(s) 35294876
Submission date Nov 06, 2020
Last update date Apr 06, 2022
Contact name Shaun Mahony
E-mail(s) mahony@psu.edu
Phone 814-865-3008
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Shaun Mahony
Street address 404 South Frear Bldg
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (48)
GSM4886908 ChIPseq SETD1A in wildtype ES cells (iCre) replicate 1
GSM4886909 ChIPseq SETD1A in wildtype ES cells (iCre) replicate 2
GSM4886910 ChIPseq NELF in wildtype ES cells (iCre) replicate 1
This SubSeries is part of SuperSeries:
GSE160966 The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes
Relations
BioProject PRJNA675001
SRA SRP291409

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
GSE160959_2iMINUS_H3K4me3_doubleKO_H3K4me3_doubleKO.p0.01.domains.txt.gz 769.6 Kb (ftp)(http) TXT
GSE160959_2iMINUS_NELF_doubleKO_NELF_doubleKO.events.txt.gz 161.0 Kb (ftp)(http) TXT
GSE160959_CHD4_2iMINUS_WT.events.txt.gz 109.9 Kb (ftp)(http) TXT
GSE160959_CHD4_2iMINUS_Zbtb11KO.events.txt.gz 72.3 Kb (ftp)(http) TXT
GSE160959_CHD4_2iMINUS_Zfp131KO.events.txt.gz 176.7 Kb (ftp)(http) TXT
GSE160959_CHD4_Zbtb11_deseq.txt.gz 585.6 Kb (ftp)(http) TXT
GSE160959_CHD4_Zfp131_deseq.txt.gz 929.8 Kb (ftp)(http) TXT
GSE160959_H3K27ac_2iMINUS_WT.domains.txt.gz 590.5 Kb (ftp)(http) TXT
GSE160959_H3K27ac_2iMINUS_Zbtb11KO.domains.txt.gz 520.4 Kb (ftp)(http) TXT
GSE160959_H3K27ac_2iMINUS_Zfp131KO.domains.txt.gz 552.5 Kb (ftp)(http) TXT
GSE160959_H3K27ac_Zbtb11_deseq.txt.gz 3.7 Mb (ftp)(http) TXT
GSE160959_H3K27ac_Zfp131_deseq.txt.gz 3.8 Mb (ftp)(http) TXT
GSE160959_H3K27me3_2iMINUS_WT.domains.txt.gz 504.5 Kb (ftp)(http) TXT
GSE160959_H3K27me3_2iMINUS_Zbtb11KO.domains.txt.gz 644.8 Kb (ftp)(http) TXT
GSE160959_H3K27me3_2iMINUS_Zfp131KO.domains.txt.gz 596.6 Kb (ftp)(http) TXT
GSE160959_H3K27me3_Zbtb11_deseq.txt.gz 4.3 Mb (ftp)(http) TXT
GSE160959_H3K27me3_Zfp131_deseq.txt.gz 4.0 Mb (ftp)(http) TXT
GSE160959_H3K4me3_2iMINUS_WT.domains.txt.gz 644.5 Kb (ftp)(http) TXT
GSE160959_H3K4me3_2iMINUS_Zbtb11KO.domains.txt.gz 602.4 Kb (ftp)(http) TXT
GSE160959_H3K4me3_2iMINUS_Zfp131KO.domains.txt.gz 587.9 Kb (ftp)(http) TXT
GSE160959_H3K4me3_Zbtb11_deseq.txt.gz 1.8 Mb (ftp)(http) TXT
GSE160959_H3K4me3_Zfp131_deseq.txt.gz 3.4 Mb (ftp)(http) TXT
GSE160959_NELF_2iMINUS_WT.events.txt.gz 870.6 Kb (ftp)(http) TXT
GSE160959_NELF_2iMINUS_Zbtb11KO.events.txt.gz 283.7 Kb (ftp)(http) TXT
GSE160959_NELF_2iMINUS_Zfp131KO.events.txt.gz 322.1 Kb (ftp)(http) TXT
GSE160959_NELF_Zbtb11_deseq.txt.gz 3.8 Mb (ftp)(http) TXT
GSE160959_NELF_Zfp131_deseq.txt.gz 3.8 Mb (ftp)(http) TXT
GSE160959_POL2S5P_2iMINUS_WT.domains.txt.gz 1.9 Mb (ftp)(http) TXT
GSE160959_RAW.tar 33.1 Gb (http)(custom) TAR (of BW)
GSE160959_SETD1A_2iMINUS_WT.events.txt.gz 317.8 Kb (ftp)(http) TXT
GSE160959_SIN3A_2iMINUS_WT.events.txt.gz 1.1 Mb (ftp)(http) TXT
GSE160959_SIN3A_2iMINUS_Zbtb11KO.events.txt.gz 834.6 Kb (ftp)(http) TXT
GSE160959_SIN3A_2iMINUS_Zfp131KO.events.txt.gz 176.7 Kb (ftp)(http) TXT
GSE160959_SIN3A_Zbtb11_deseq.txt.gz 6.9 Mb (ftp)(http) TXT
GSE160959_SIN3A_Zfp131_deseq.txt.gz 3.7 Mb (ftp)(http) TXT
GSE160959_Zbtb11_2iPLUS.events.txt.gz 330.7 Kb (ftp)(http) TXT
GSE160959_Zfp131_2iPLUS.events.txt.gz 59.8 Kb (ftp)(http) TXT
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