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Genomic and functional characterization of histone H3 lysine 4 methylation co-localized marks | Lv 1 | Computational Molecular Biology

Genomic and functional characterization of histone H3 lysine 4 methylation co-localized marks  

Jie Lv1 , Hongbo Liu1 , Hui Liu1 , Qiong Wu1 , Yan Zhang2
1. School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
2. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
Author    Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 10   doi: 10.5376/cmb.2014.04.0010
Received: 07 Sep., 2014    Accepted: 25 Oct., 2014    Published: 14 Nov., 2014
© 2014 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Lv et al., 2014, Genomic and functional characterization of histone H3 lysine 4 methylation co-localized marks, Computational Molecular Biology, Vol.4, No.10, 1-17 (doi: 10.5376/cmb.2014.04.0010)

Abstract

Histone modifications play important roles in dynamic transcription regulation. In mammals, methylation of lysine 4 in histone H3 (H3K4) is associated with open chromatin environment. From functional genomic perspective, the combinations of methylation co-localized marks in lysine residue 4 of histone H3 (H3K4me) are little studied. The genomic patterns of specific H3K4me co-localized peaks are highly conserved. Additionally, the proteins encoded by genes with co-localization peaks in promoter regions have more partners in protein-protein interaction network. We also found the unbalanced base composition, that is, AT nucleotide is preferred in genomic regions with co-localization H3K4me modifications. Gene Ontology enrichment analysis revealed that genes with specific co-localization modifications in promoter regions are function-specific. We also found the PolII level for different combinations are correlated with the differential methyl accumulation of H3K4. Me1me2me3, the triplet for H3K4me, is associated with tissue specificity. This study helps understanding the genomic features of H3K4me co-localization and the role of H3K4me co-localization in function genomic regulation.

Keywords
Histone modifications; Co-localization; Genomic composition; CpG islands; H3K4me
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