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Series GSE67520 Query DataSets for GSE67520
Status Public on Dec 31, 2015
Title Oct4 binding and Histone modification profiling during OSKM-mediated 2nd reprogramming
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors. To address this gap,we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification (H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. Through integrative analysis, we revealed stage-specific Oct4 binding and enhancer signatures in consistence with gene expression changes, in which the initial regression of somatic program is followed by the gradual acquisition of pluripotent program. Oct4 preferatially binds to H3K4me1 marked enhancer regions and Oct4 binding is positively correlated with active mark H3K27ac. Moreover, we observed significant enhancer activation of epigenetic related genes, especially acetylation associated genes, prior to pluripotency network activation, suggesting a pivotal role of epigenetic remodelling in the process of pluripotency acquisition and maintenance.
Overall design We used ChIP-seq to explore the global changes of Oct4 binding profiling during OSKM-mediated somatic cell reprogramming. The exogenous Oct4 was tagged with 3XFlag, thus we used anti-flag antibody to monitor exogenous Oct4 changes; anti-Oct4 antibody which recognizes both endogenous and exogenous Oct4 was used to monitor total Oct4 changes during iPSC induction. In addition, we also examined genome-wide H3K4me1/H3K27ac/H3K4me3/H3K27me3/RNAPII profiling during 3Flag-OSKM 2' reprogramming.
Citation(s) 26832419
Submission date Apr 01, 2015
Last update date May 15, 2019
Contact name Min Li
Organization name Tongji University
Street address 1239 Siping Road, Yangpu District
City Shanghai
ZIP/Postal code 200092
Country China
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (71)
GSM1648616 flag_Oct4_ChipSeq_day0
GSM1648617 flag_Oct4_ChipSeq_day1
GSM1648618 flag_Oct4_ChipSeq_day3
BioProject PRJNA280196
SRA SRP056828

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Supplementary file Size Download File type/resource
GSE67520_RAW.tar 63.5 Mb (http)(custom) TAR (of BED, BROADPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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