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Series GSE169044 Query DataSets for GSE169044
Status Public on Nov 21, 2022
Title Transcription factor antagonism regulates heterogeneity in embryonic stem cell states
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Gene expression heterogeneity underlies the formation of cell states, and switching between states contributes to developmental robustness. While gene expression variation can arise from stochastic transcriptional processes, whether it can be regulated and coordinated by an underlying program is unclear. We characterize the regulatory program underlying heterogeneity and switching between murine embryonic stem cell (mESC) states. Using nascent transcriptome assays, we identified a subset of differentially active and transcribed enhancers (DATEs) across states. DATEs regulate variably expressed gene targets and contribute to cell state formation. Further, DATEs are distinguished by co-binding of Kruppel-like transcription factors Klf4 and Zfp281. In contrast to other transcription factors that form a positive feedback network stabilizing ES cell-type identity, Klf4 and Zfp281 drive opposing transcriptional and chromatin programs. Abrogation of their ability to bind DATEs dampens variation in gene expression and reduces heterogeneity. Single cell analysis reveals competing Klf4 and Zfp281 gene programs that define mESC state, consistent with a model whereby Klf4 and Zfp281 generate transcriptional heterogeneity through functional antagonism at DATEs. These results show how antagonistic circuits of TFs and enhancers contributes to gene expression variation and cell state, with potential implications for the generation of diverse cell types during mammalian development.
 
Overall design (1) Examination of nascent transcriptome by mPROseq in three mESC states defined by Nanog- and Sox2-defined subpopulations (States 1, 2, and 3) in three biological replicates;
(2) Examination of nascent transcriptome by mPROseq in WT, Klf4KO, Zfp281KO mESC in three biological replicates;
(3) Examination of steady state transcriptome by RNAseq in WT, Klf4KO, Zfp281KO mESC in nine biological replicates;
(4) Examination of chromatin accessibility by ATACseq in WT, Klf4KO, Zfp281KO mESC in three biological replicates;
(5) ChIPseq of Klf4 and Zfp281 in WT, Klf4KO, Zfp281KO mESC;
(6) Single cell RNA sequencing of two biological replicates each of WT, Klf4KO, Zfp281KO mESC
(7) CUT&RUN of Klf4 and Zfp281 in States 1, 2, and 3
 
Contributor(s) Hu S, Garg S
Citation(s) 36356583
NIH grant(s)
Grant ID Grant title Affiliation Name
F30 CA260739 Role of a Two-Factor Genetic Circuit Regulating Stemness in Colorectal Cancer HARVARD UNIVERSITY (MEDICAL SCHOOL) Sofia Hu
K08 CA237856 Mechanisms of non-genetic variation in melanoma MASSACHUSETTS GENERAL HOSPITAL Salil Garg
Submission date Mar 16, 2021
Last update date Feb 20, 2023
Contact name Sofia Hu
E-mail(s) sofiahu@mit.edu
Organization name MIT
Street address 500 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (3)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (101)
GSM5175674 scATACseq_ESC
GSM5175675 mPROseq_ESC_State1_BR1
GSM5175676 mPROseq_ESC_State1_BR2
Relations
BioProject PRJNA714958
SRA SRP310947

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE169044_RAW.tar 14.8 Gb (http)(custom) TAR (of BIGWIG, TAR)
GSE169044_metadata_update.xlsx 98.1 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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