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SRX276673: GSM1138457: NSC_H3K27me3; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina Genome Analyzer) run: 21.8M spots, 762.4M bases, 415.9Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: An epigenetic signature of developmental potential in neural stem cells and early neurons [ChIP-seq]
show Abstracthide Abstract
A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). Bivalency has subsequently emerged as a powerful epigenetic indicator of stem cell potential. Here, we have interrogated the epigenome during differentiation of ESC-derived NSCs to immature GABAergic interneurons. We show that developmental transitions are accompanied by loss of bivalency at many promoters in line with their increasing developmental restriction from pluripotent ESC through multipotent NSC to committed GABAergic interneuron. At the NSC stage, the promoters of genes encoding many transcriptional regulators required for differentiation of multiple neuronal subtypes and neural crest appear to be bivalent, consistent with the broad developmental potential of NSCs. Upon differentiation to GABAergic neurons, all non-GABAergic promoters resolve to H3K27me3 monovalency, whereas GABAergic promoters resolve to H3K4me3 monovalency or retain bivalency. Importantly, many of these epigenetic changes occur prior to any corresponding changes in gene expression. Intriguingly, another group of gene promoters gain bivalency as NSCs differentiate toward neurons, the majority of which are associated with functions connected with maturation and establishment and maintenance of connectivity. These data show that bivalency provides a dynamic epigenetic signature of developmental potential in both NSCs and in early neurons. Overall design: Neural stem cells derived from mouse embryonic stem cells were differentiated into neurons and FACS purified based on RedStar fluorescence driven by the Tau promoter. Chromatin was prepared from NSCs and neurons (n=1), sonicated to roughly 300bp and immunoprecipitated with antibodies against H3K4me3, H3K27me3, total Histone H3 and total IgG, alongside a 5% input sample. K4/K27 and corresponding input samples were analysed by ChIPSeq
Sample: NSC_H3K27me3
SAMN02141700 • SRS419866 • All experiments • All runs
Organism: Mus musculus
Instrument: Illumina Genome Analyzer
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: Cells were fixed in 1% HCHO and lysed in 1% SDS lysis buffer. Chromatin was sheared to 300bp and immunoprecipitated with antibodyies against H3K4me3, H3K27me3, total histone H3 and IgG. Total H3 was from Abcam (ab1791) and rabbit IgG from Santa Cruz (SC-2027) were used to precipitate all samples, in addition to the IPs done with H3K4me3 and H3K27me3. Only the K4/K27 were sequenced. Libraries were prepared according to standard Illumina Solexa protocols
Experiment attributes:
GEO Accession: GSM1138457
External link:
Runs: 1 run, 21.8M spots, 762.4M bases, 415.9Mb
Run# of Spots# of BasesSizePublished


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