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

Xiao-Long Cui, Ji Nie, Jeremy Ku, Urszula Dougherty, Diana C. West-Szymanski, Francois Collin, Christopher K. Ellison, Laura Sieh, Yuhong Ning, Zifeng Deng, Carolyn W. T. Zhao, Anna Bergamaschi, Joel Pekow, Jiangbo Wei, Alana V. Beadell, Zhou Zhang, Geeta Sharma, Raman Talwar, Patrick Arensdorf, Jason Karpus, Ajay Goel, Marc Bissonnette, Wei Zhang, Samuel Levy and Chuan He ()
Additional contact information
Xiao-Long Cui: University of Chicago
Ji Nie: University of Chicago
Jeremy Ku: Bluestar Genomics Inc.
Urszula Dougherty: University of Chicago
Diana C. West-Szymanski: University of Chicago
Francois Collin: Bluestar Genomics Inc.
Christopher K. Ellison: Bluestar Genomics Inc.
Laura Sieh: University of Chicago
Yuhong Ning: Bluestar Genomics Inc.
Zifeng Deng: University of Chicago
Carolyn W. T. Zhao: University of Chicago
Anna Bergamaschi: Bluestar Genomics Inc.
Joel Pekow: University of Chicago
Jiangbo Wei: University of Chicago
Alana V. Beadell: University of Chicago
Zhou Zhang: Northwestern University Feinberg School of Medicine
Geeta Sharma: City of Hope Comprehensive Cancer Center
Raman Talwar: Bluestar Genomics Inc.
Patrick Arensdorf: Bluestar Genomics Inc.
Jason Karpus: University of Chicago
Ajay Goel: City of Hope Comprehensive Cancer Center
Marc Bissonnette: University of Chicago
Wei Zhang: Northwestern University Feinberg School of Medicine
Samuel Levy: Bluestar Genomics Inc.
Chuan He: University of Chicago

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract 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.

Date: 2020
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-020-20001-w Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20001-w

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-20001-w

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().