Genomics,Multiomics

Dataset Information

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4Cseq analysis of neural stem/progenitor cells (NSC) from wild type and Sox2-deleted mouse neonatal forebrain


ABSTRACT: We report the application of 4Cseq technology for the profiling of chromatin interactions in wild type and Sox2-deleted NSC, for 9 different loci (viewpoints): Olig2 promoter, Olig1 promoter, Tcf4 promoter, Kat2b promoter, Sox3 promoter, Stox2 promoter, c-fos 5' enhancer, c-fos 3' enhancer and c-fos promoter. Overall design: NSC from wild type and mutant littermates individual mouse forebrains were cultured, and expanded for 3-7 passages (as in Favaro et al., Nature Neuroscience 2009, 12:1248-56, and Zhang et al., Nature 2013, 504:306-10). Cells were fixed as in Zhang et al., 2013, and processed for 4Cseq analysis. For 7 viewpoints analyzed, three wild type and three mutant cultures, each derived from individual P0 brains of littermate mice, were used; for 2 viewpoints analyzed, one wild type and one mutant culture were used.

INSTRUMENT(S): Illumina NextSeq 500 (Mus musculus)

ORGANISM(S): Mus musculus  

SUBMITTER: Federico Zambelli 

PROVIDER: GSE111190 | GEO | 2019-03-07

REPOSITORIES: GEO

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Publications


The SOX2 transcription factor is critical for neural stem cell (NSC) maintenance and brain development. Through chromatin immunoprecipitation (ChIP) and chromatin interaction analysis (ChIA-PET), we determined genome-wide SOX2-bound regions and Pol II-mediated long-range chromatin interactions in brain-derived NSCs. SOX2-bound DNA was highly enriched in distal chromatin regions interacting with promoters and carrying epigenetic enhancer marks. Sox2 deletion caused widespread reduction of Pol II-  ...[more]

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