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| Status |
Public on Oct 28, 2020 |
| Title |
A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
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 herein, the development of a 5hmC tissue map by characterizing 5hmC genomic distributions in 19 human tissues derived from 10 organ systems. Subsequent sequencing results enabled the identification of genome-wide 5hmC distributions that uniquely separated donor samples by tissue type. Further comparison of 5hmC profiles with transcriptomes and histone modifications revealed that 5hmC was preferentially enriched on tissue-specific gene bodies and enhancers. Taken together, we report herein an extensive 5hmC map across diverse human tissue types and suggest an important role of 5hmC in tissue-specific development by integration with public epigenomic data. This resource will facilitate future studies of DNA demethylation in pathogenesis and development of 5hmC as biomarkers for various human diseases.
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| |
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| Overall design |
We generated genomic 5hmC-Seal and RNA-seq profiles of 19 human tissues and compared with other reference epigenomic data.
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| |
|
| Contributor(s) |
Cui X, Nie J, Ku J, Levy S, He C |
| Citation(s) |
33268789 |
| |
| Submission date |
Jan 30, 2020 |
| Last update date |
Dec 05, 2020 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (192)
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| Relations |
| BioProject |
PRJNA603959 |
| SRA |
SRP246098 |
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