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Series GSE34906 Query DataSets for GSE34906
Status Public on Mar 26, 2012
Title Genetic and epigenetic determinants of neurogenesis and myogenesis [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wide binding and transcription profiles of NEUROD2-mediated neurogenesis with MYOD-mediated myogenesis. We demonstrate that NEUROD2 and MYOD bind a shared CAGCTG E-box motif and E-box motifs specific for each factor: CAGGTG for MYOD and CAGATG for NEUROD2. Binding at factor-specific motifs is associated with gene transcription, whereas binding at shared sites is associated with regional epigenetic modifications but not as strongly associated with gene transcription. Binding is largely constrained to E-boxes pre-set in an accessible chromatin context that determines the set of target genes activated in each cell type. These findings demonstrate that the differentiation program is genetically determined by E-box sequence whereas cell lineage epigenetically determines the availability of E-boxes for each differentiation program.
Overall design Comparing NeuroD2 induced neurogenesis and MyoD induced myogenesis by examining NeuroD2/MyoD binding sites in fibroblasts and P19 cells and corresponding changes in AcH4 using Chip-Seq. Assess chromatin accessibility using PvuII assay followed by high throughput sequencing.
Contributor(s) Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ
Citation(s) 22445365, 23566431
Submission date Jan 06, 2012
Last update date Aug 23, 2019
Contact name Stephen Tapscott
Organization name Fred Hutch Cancer Research Center
Department Human Biology
Lab Tapscott
Street address 1100 Fairview N. Ave
City Seattle
State/province WASHINGTON
ZIP/Postal code 98103
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (9)
GSM857388 P19 control
GSM857389 P19 with NeuroD2
GSM857390 P19 with MyoD
This SubSeries is part of SuperSeries:
GSE34908 Genetic and epigenetic determinants of neurogenesis and myogenesis
SRA SRP010165
BioProject PRJNA156259

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Supplementary file Size Download File type/resource
GSE34906_RAW.tar 7.2 Gb (http)(custom) TAR (of BAM, BEDGRAPH, MAP)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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