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Series GSE90893 Query DataSets for GSE90893
Status Public on Jan 19, 2017
Title Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Oct4, Sox2, Klf4, and cMyc (OSKM) reprogram somatic cells to pluripotency. To gain a mechanistic understanding of their function, we mapped OSKM-binding, stage-specific transcription-factors (TFs), and chromatin-states in discrete reprogramming stages and performed loss- and gain-of-function experiments. We found that early in reprogramming OSK extensively bind somatic-enhancers and initiate their decommissioning by recruiting Hdac1. Concurrently, OSK engage other sites, including specific pluripotency-enhancers, and induce the relocation of somatic TFs to these sites and away from somatic-enhancers, extending somatic-enhancer decommissioning genome-wide. Pluripotency-enhancer selection early in reprogramming occurs predominantly at sites with high OSK-motif densities and requires collaborative binding by OSK. Most pluripotency-enhancers are selected later and occupied by OS and stage-specific-TFs like Esrrb. Overexpression of stage-specific-TFs influences reprogramming efficiency by changing OSK-occupancy, somatic-enhancer decommissioning, and pluripotency-enhancer selection. We propose that collaborative interactions among OSK and with stage-specific-TFs direct both somatic-enhancer decommissioning and pluripotency-enhancer selection, which drives the enhancer reorganization underlying reprogramming
 
Overall design Examination of 9 different histone modifications, 1 histone variant, the histone H3, 10 transcription factors and 3epigenetic regulators in 4 cell types.
 
Contributor(s) Chronis C, Fiziec P, Papp B, Butz S, Bonora G, Sabri S, Ernst J, Plath K
Citation(s) 28111071
Submission date Dec 05, 2016
Last update date Dec 18, 2020
Contact name Kathrin Plath
Organization name UCLA
Street address BOX 951737, 36-133 CHS
City Los Angeles
State/province CA
ZIP/Postal code 90095-1737
Country USA
 
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (119)
GSM2417077 MEF_H3K4me3_ChIP-Seq
GSM2417078 48h_H3K4me3_ChIP-Seq
GSM2417079 preiPSC#1_H3K4me3_ChIP-Seq
This SubSeries is part of SuperSeries:
GSE90895 Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming
Relations
BioProject PRJNA356297
SRA SRP094580

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
GSE90893_Peak_calls_table.xls.gz 41.4 Mb (ftp)(http) XLS
GSE90893_RAW.tar 5.6 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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