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Gene Regulation and Systems Biology

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Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq

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Publication Date: 20 Jan 2014

Type: Original Research

Journal: Gene Regulation and Systems Biology

Citation: Gene Regulation and Systems Biology 2014:8 33-43

doi: 10.4137/GRSB.S13612

Abstract

Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.


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What Your Colleagues Say About Gene Regulation and Systems Biology
The reviewing and editorial management of our paper was timely, thorough, and systematic.  In particular the reviewers' comments resulted in a paper significantly more robust than the first version.
Dr Clark D Jeffries (University of North Carolina at Chapel Hill, Chapel Hill, NC, USA)
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