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Large-scale determination and characterization of cell type-specific regulatory elements in the human genome Free
Can Wang 1,2 and Shihua Zhang 1,2,*
1 NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China

2 School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China *Correspondence to:Shihua Zhang, E-mail: zsh@amss.ac.cn
J Mol Cell Biol, Volume 9, Issue 6, December 2017, Pages 463-476  https://doi.org/10.1093/jmcb/mjx058
Keyword: epigenomics, histone modification, cell type-specific regulatory elements, bioinformatics

Histone modifications have been widely elucidated to play vital roles in gene regulation and cell identity. The Roadmap Epigenomics Consortium generated a reference catalog of several key histone modifications across >100s of human cell types and tissues. Decoding these epigenomes into functional regulatory elements is a challenging task in computational biology. To this end, we adopted a differential chromatin modification analysis framework to comprehensively determine and characterize cell type-specific regulatory elements (CSREs) and their histone modification codes in the human epigenomes of five histone modifications across 127 tissues or cell types. The CSREs show significant relevance with cell type-specific biological functions and diseases and cell identity. Clustering of CSREs with their specificity signals reveals distinct histone codes, demonstrating the diversity of functional roles of CSREs within the same cell or tissue. Last but not least, dynamics of CSREs from close cell types or tissues can give a detailed view of developmental processes such as normal tissue development and cancer occurrence.