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.

Gene regulation and systems biology Pub Date : 2014-01-20 eCollection Date: 2014-01-01 DOI:10.4137/GRSB.S13612
Ngoc Tam L Tran, Chun-Hsi Huang
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引用次数: 3

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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H3K4me3和H3K4me1在小鼠肝脏和小鼠胚胎干细胞中的基因表达及基因本体富集分析
最近的研究已经确定了小鼠基因组中的顺式调控元件及其基因组定位。最近的发现表明,H3赖氨酸4三甲基化(H3K4me3)结合作为活性启动子的富集,以及H3赖氨酸4单甲基化(H3K4me1)在启动子区域外的存在作为增强子的标志。在本研究中,我们利用ChIP-Seq和RNA-Seq进一步鉴定了小鼠肝脏中H3K4me3标记或H3K4me3和H3K4me1标记的高表达基因。我们发现,在小鼠中,肝脏具有胚胎干细胞相关功能,而胚胎干细胞也具有肝脏相关功能。我们还在小鼠肝脏和小鼠胚胎干细胞的RNA-Seq实验中发现了新的基因。这些基因目前不在NCBI的Ensemble基因数据库中。
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