Sridharan2013 Data: Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-HP1gamma in reprogramming to pluripotency

By (Secondary Ownership. The experiment uses only third-party data.)

Abstract from Pubmed:

Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) involves a marked reorganization of chromatin. To identify post-translational histone modifications that change in global abundance during this process, we have applied a quantitative mass-spectrometry-based approach. We found that iPSCs, compared with both the starting fibroblasts and a late reprogramming intermediate (pre-iPSCs), are enriched for histone modifications associated with active chromatin, and depleted for marks of transcriptional elongation and a subset of repressive modifications including H3K9me2/me3. Dissecting the contribution of H3K9 methylation to reprogramming, we show that the H3K9 methyltransferases Ehmt1, Ehmt2 and Setdb1 regulate global H3K9me2/me3 levels and that their depletion increases iPSC formation from both fibroblasts and pre-iPSCs. Similarly, we find that inhibition of heterochromatin protein-1gamma (Cbx3), a protein known to recognize H3K9 methylation, enhances reprogramming. Genome-wide location analysis revealed that Cbx3 predominantly binds active genes in both pre-iPSCs and pluripotent cells but with a strikingly different distribution: in pre-iPSCs, but not in embryonic stem cells, Cbx3 associates with active transcriptional start sites, suggesting a developmentally regulated role for Cbx3 in transcriptional activation. Despite largely non-overlapping functions and the predominant association of Cbx3 with active transcription, the H3K9 methyltransferases and Cbx3 both inhibit reprogramming by repressing the pluripotency factor Nanog. Together, our findings demonstrate that Cbx3 and H3K9 methylation restrict late reprogramming events, and suggest that a marked change in global chromatin character constitutes an epigenetic roadblock for reprogramming.
Cbx3 pre-iPS iPS heterochromatin ChIP-seq chromatin remodeling Nanog reprogramming
Show history? PUBLIC
Illumina HiSeq 2000

Some things you might want to do with these data..

Input Data

Sample Groups and Experimental Factors

Genome Snapshots

'Genome snapshots' are assorted genomic regions that the creators of this experiment considered of particular interest.

Pou5f1 Locus

Nanog Locus

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Other data generated in this experiment:

Typical analysis workflows my generate dozens or even hundreds of outputs. To condense the amount of information into more easily digestible portions, GeneProf will, by default, only display the experiments input data (here: input data) and a selection of the most important outputs (here: main results). You can drill down into the details of the analysis via the workflow designer or you can display other intermediate outputs here.

Analysis Workflow

This is a schematic representation of the analysis workflow used in this experiment. For more details (parameters, etc.) use the fully-featured workflow designer.
Colours represent types of data (sequences, genomic regions, features, references and files.
Get a simple, static workflow diagram as PNG | JPEG | PDF | SVG | EPS, or get the complete, detailed version as PNG | JPEG | PDF | SVG | EPS.