Mouse Gene Set: MIKKELSEN_ES_LCP_WITH_H3K4ME3

For the Human gene set with the same name, see MIKKELSEN_ES_LCP_WITH_H3K4ME3

Standard name MIKKELSEN_ES_LCP_WITH_H3K4ME3
Systematic name MM858
Brief description Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in embryonic stem cells (ES).
Full description or abstract We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Collection M2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 17603471   Authors: Mikkelsen TS,Ku M,Jaffe DB,Issac B,Lieberman E,Giannoukos G,Alvarez P,Brockman W,Kim TK,Koche RP,Lee W,Mendenhall E,O'Donovan A,Presser A,Russ C,Xie X,Meissner A,Wernig M,Jaenisch R,Nusbaum C,Lander ES,Bernstein BE
Exact source Table 4S: Class=LCP & ESC state=K4
Related gene sets (show 15 additional gene sets from the source publication)

(show 42 gene sets from the same authors)
External links
Filtered by similarity ?
Source species Mus musculus
Contributed by Arthur Liberzon (MSigDB Team)
Source platform or
identifier namespace		 MOUSE_GENE_SYMBOL
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 ? NG-CHM interactive heatmaps
(Please note that clustering takes a few seconds)
Mouse Transcriptomic BodyMap compendium

Legacy heatmaps (PNG)
Mouse Transcriptomic BodyMap compendium
Advanced query Further investigate these 147 genes
Show members (show 151 source identifiers mapped to 147 genes)
Version history 2022.1.Mm: First Introduced.

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