Novel Comparative Pattern Count Analysis Reveals a Chronic Ethanol Induced Dynamic Shift In NF-κB Genome-wide Promoter Binding During Liver Regeneration

ABSTRACT: We analyzed the effect of chronic alcohol intake on the genome-wide binding activity of NF-κB during the initial response phase following partial hepatectomy. We analyzed the data in the adapted state as well as in response to partial hepatectomy, using chromatin immunoprecipitation followed by promoter microarray analysis. We found several ethanol-specific NF-κB binding target promoters in the chronic adapted state.. Partial hepatectomy induced a diet-independent shift in NF-κB binding loci relative to the transcription start sites. We employed a novel pattern count analysis to exhaustively enumerate and compare the number of promoters corresponding to the temporal binding patterns between ethanol and isocaloric pair-fed control groups. We found that NF-κB bound genes govern negative regulation of cell growth and inflammatory response immediately following hepatectomy. We, integrated the ChIP-chip results with a time series gene expression data set to identify the NF-κB promoter binding targets that showed differential gene expression changes at the baseline-adapted condition as well as after PHx. We identified a set of differential patterns of NF-κB binding that were specific to the ethanol and pair-fed control groups. We found the regulatory pathways and co-incident transcription factor binding motifs corresponding some of the key comparative-binding patterns.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE74273 | GEO | 2015/10/23

SECONDARY ACCESSION(S): PRJNA299606

REPOSITORIES: GEO