Journal Article

A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation

Ning, Yuhong, Collin, Francois, Nie, Ji, Sieh, Laura, Zhao, Carolyn W. T., Bissonnette, Marc, Cui, Xiao-Long, Karpus, Jason, Arensdorf, Patrick, Sharma, Geeta, Levy, Samuel, Deng, Zifeng, Goel, Ajay, Zhang, Zhou, Zhang, Wei, West-Szymanski, Diana C., He, Chuan, Ku, Jeremy, Bergamaschi, Anna, Ellison, Christopher K., Pekow, Joel, Talwar, Raman, Beadell, Alana V., Dougherty, Urszula, Wei, Jiangbo

2020

Overview

DNA 5-hydroxymethylcytosine (5hmC) modification is known to be associated with gene transcription and frequently used as a mark to investigate dynamic DNA methylation conversion during mammalian development and in human diseases. However, the lack of genome-wide 5hmC profiles in different human tissue types impedes drawing generalized conclusions about how 5hmC is implicated in transcription activity and tissue specificity. To meet this need, we describe the development of a 5hmC tissue map by characterizing the genomic distributions of 5hmC in 19 human tissues derived from ten organ systems. Subsequent sequencing results enabled the identification of genome-wide 5hmC distributions that uniquely separates samples by tissue type. Further comparison of the 5hmC profiles with transcriptomes and histone modifications revealed that 5hmC is preferentially enriched on tissue-specific gene bodies and enhancers. Taken together, the results provide an extensive 5hmC map across diverse human tissue types that suggests a potential role of 5hmC in tissue-specific development; as well as a resource to facilitate future studies of DNA demethylation in pathogenesis and the development of 5hmC as biomarkers. DNA 5-hydroxymethylcytosine (5hmC) modification is associated with gene transcription and used as a mark of mammalian development. Here the authors report a comprehensive 5hmC tissue map and analysis of 5hmC genomic distributions in 19 human tissues derived from 10 organ systems, thus providing insights into the role of 5hmC in tissue-specific development.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/15 / 45/91 / 49/23 / 5-Methylcytosine - analogs & derivatives / 5-Methylcytosine - metabolism / 631/208/176/1988 / 631/208/177 / 631/337/1644 / Biomarkers / Chromosome Mapping / CpG Islands / Cytosine - metabolism / Demethylation / Deoxyribonucleic acid / DNA / DNA - genetics / DNA - metabolism / DNA Methylation / Enhancer Elements, Genetic / Enhancers / Epigenesis, Genetic / Genome, Human / Genomes / Genomic analysis / Histones / Histones - genetics / Histones - metabolism / Human tissues / Humanities and Social Sciences / Humans / Mammals / multidisciplinary / Organ Specificity / Pathogenesis / Science / Science (multidisciplinary) / Tissues / Transcription / Transcription Factors - genetics / Transcription Factors - metabolism / Transcriptional Activation