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Series GSE160960 Query DataSets for GSE160960
Status Public on Jan 07, 2022
Title The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [RNA-Seq]
Organism Mus musculus
Experiment type Expression 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 binding, 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 (28)
GSM4886952 RNAseq in Wildtype ES grown in +2i+LIF replicate 1
GSM4886953 RNAseq in Wildtype ES grown in +2i+LIF replicate 2
GSM4886954 RNAseq in Wildtype ES grown in -2i+LIF 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 PRJNA675002
SRA SRP291406

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
GSE160960_WTvsDKO_minus.results.txt.gz 857.3 Kb (ftp)(http) TXT
GSE160960_WTvsDKO_plus.results.txt.gz 850.2 Kb (ftp)(http) TXT
GSE160960_WTvsZ10KO_doxminus.results.txt.gz 818.4 Kb (ftp)(http) TXT
GSE160960_WTvsZ10KO_doxplus.results.txt.gz 834.2 Kb (ftp)(http) TXT
GSE160960_WTvsZ10KO_minus.results.txt.gz 811.3 Kb (ftp)(http) TXT
GSE160960_WTvsZ10KO_plus.results.txt.gz 796.3 Kb (ftp)(http) TXT
GSE160960_WTvsZ11KO_doxminus.results.txt.gz 850.5 Kb (ftp)(http) TXT
GSE160960_WTvsZ11KO_doxplus.results.txt.gz 1.3 Mb (ftp)(http) TXT
GSE160960_WTvsZ11KO_minus.results.txt.gz 851.6 Kb (ftp)(http) TXT
GSE160960_WTvsZ11KO_plus.results.txt.gz 857.2 Kb (ftp)(http) TXT
GSE160960_WTvsZ131KO_doxminus.results.txt.gz 845.9 Kb (ftp)(http) TXT
GSE160960_WTvsZ131KO_doxplus.results.txt.gz 828.1 Kb (ftp)(http) TXT
GSE160960_WTvsZ131KO_minus.results.txt.gz 846.2 Kb (ftp)(http) TXT
GSE160960_WTvsZ131KO_plus.results.txt.gz 819.7 Kb (ftp)(http) TXT
GSE160960_Z11vsDKO_minus.results.txt.gz 856.8 Kb (ftp)(http) TXT
GSE160960_Z11vsDKO_plus.results.txt.gz 871.0 Kb (ftp)(http) TXT
GSE160960_Z131vsDKO_minus.results.txt.gz 1.2 Mb (ftp)(http) TXT
GSE160960_Z131vsDKO_plus.results.txt.gz 1.2 Mb (ftp)(http) TXT
GSE160960_featurecounts.txt.gz 3.5 Mb (ftp)(http) TXT
GSE160960_mES-ZBTB.featurecounts.out.txt.gz 4.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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