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| Status |
Public on Dec 13, 2015 |
| Title |
Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We investigated genome-wide nucleosome coverage and histone methylation occupancies in somatic MEFs, intermediate pre-iPSCs and fully reprogrammed iPSCs. We found that nucleosome occupancies increased in promoter regions and decreased in intergenic regions in pre-iPSCs and then recover to an intermediate level in iPSCs. Nucleosomes in pre-iPSCs are much more phased than those in MEFs and iPSCs. Bivalent, active, repressive domains are cell type-specific and change dynamically during reprogramming. HCG and LCG promoters exhibit distinct nucleosome occupancy patterns and are dynamically marked by H3K4me3/H3K27me3 during reprogramming, correspondingly showing different gene activities. Surprisingly, Vitamin C promotes nucleosome reorganization from pre-iPSCs to iPSCs. CTCF binding sites change dynamically during reprogramming, though they share a conserved binding motif. Nucleosome occupies CTCF sites to a higher extent in pre-iPSCs than those in MEFs and iPSCs. Taken together, our study reveals that dynamic changes of nucleosome positioning and chromatin organization associated gene regulation during reprogramming.
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| Overall design |
Examine dynamics of nucleosome positioning and histone modification profiles as well as gene expression regulation during somatic cell reprogramming
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| Contributor(s) |
Huang K, Zhang X, Shi J, Yao M, Lin J, Li J, He L, Li H, Shi G, Wang Z, Zhang B, Chen J, Pan G, Jiang C, Pei D, Yao H |
| Citation(s) |
26639176 |
| Submission date |
Aug 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaobai Zhang |
| E-mail(s) |
zhangxb@tongji.edu.cn
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| Organization name |
Tongji University
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| Street address |
1239 Siping Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (27)
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| Relations |
| BioProject |
PRJNA258668 |
| SRA |
SRP045688 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60627_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE60627_gene_expression.txt.gz |
573.7 Kb |
(ftp)(http) |
TXT |
| GSE60627_rep.gene_expression.txt.gz |
574.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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