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ChIP-seq analysis of GATA4 in whole liver of adult mice

ABSTRACT: GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver.

ORGANISM(S): Mus musculus

PROVIDER: GSE49131 | GEO | 2013/11/07

SECONDARY ACCESSION(S): PRJNA213132

REPOSITORIES: GEO

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ChIP-seq analysis of GATA4 in whole liver of adult mice

Project description:GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver. ChIP-sequencing of whole mouse livers from 2-3 month old mice

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GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27.

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