Human Gene Set: MIKKELSEN_IPS_WITH_HCP_H3K27ME3

For the Mouse gene set with the same name, see MIKKELSEN_IPS_WITH_HCP_H3K27ME3

Standard name MIKKELSEN_IPS_WITH_HCP_H3K27ME3
Systematic name M1967
Brief description Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 (induced pluripotent cells, iPS).
Full description or abstract Somatic cells can be reprogrammed to a pluripotent state through the ectopic expression of defined transcription factors. Understanding the mechanism and kinetics of this transformation may shed light on the nature of developmental potency and suggest strategies with improved efficiency or safety. Here we report an integrative genomic analysis of reprogramming of mouse fibroblasts and B lymphocytes. Lineage-committed cells show a complex response to the ectopic expression involving induction of genes downstream of individual reprogramming factors. Fully reprogrammed cells show gene expression and epigenetic states that are highly similar to embryonic stem cells. In contrast, stable partially reprogrammed cell lines show reactivation of a distinctive subset of stem-cell-related genes, incomplete repression of lineage-specifying transcription factors, and DNA hypermethylation at pluripotency-related loci. These observations suggest that some cells may become trapped in partially reprogrammed states owing to incomplete repression of transcription factors, and that DNA de-methylation is an inefficient step in the transition to pluripotency. We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 18509334   Authors: Mikkelsen TS,Hanna J,Zhang X,Ku M,Wernig M,Schorderet P,Bernstein BE,Jaenisch R,Lander ES,Meissner A
Exact source Table 2S: Promoter=HCP & MCV8.1=K27
Related gene sets (show 20 additional gene sets from the source publication)

(show 599 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Jessica Robertson (MSigDB Team)
Source platform or
identifier namespace		 Mouse_RefSeq
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 103 genes
Gene families ? Categorize these 103 genes by gene family
Show members (show 104 source identifiers mapped to 103 genes)
Version history 3.1: First introduced

We need your help: Update on GSEA/MSigDB funding support

Last November we submitted a proposal to NCI's Information Technology for Cancer Research (ITCR) program for the continued funding of GSEA and MSigDB. Unfortunately, our proposal was not funded in this round, but we were encouraged to resubmit for the next one. This funding is critical for our continuing support and enhancement of the GSEA-MSigDB resource.

For our original submission many of you sent us emails of support, an important requirement for these grants. We now ask for your help again. We would greatly appreciate a short email message from you describing how the resource has been of value to your work and any concerns you may have about its continued availability.

Please send us your message of support to gsea-los@broadinstitute.org on or before Monday June 5, 2023.

Thanks in advance for your help and support.
The GSEA/MSigDB Team.


See MSigDB license terms here. Please note that certain gene sets have special access terms.