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

• Published in: Gene Regulation and Systems Biology Vol. 2014; no. 8; pp. 33 - 43
• Main Authors: Tran, Ngoc Tam L., Huang, Chun-Hsi
• Format: Journal Article
• Language: English
• Published: London, England Libertas Academica 01-01-2014; SAGE Publishing; SAGE Publications; Sage Publications Ltd
• Subjects: Original Research; gene ontology; ChIP-Seq; H3K4me1; RNA-Seq; H3K4me3; gene expression
• ISSN: 1177-6250; 1177-6250
• DOI: 10.4137/GRSB.S13612

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.