Epigenetic patterns in a complete human genome-Reference-Cited by-同舟云学术

Epigenetic patterns in a complete human genome

Published:2022-04 Issue:6588 Volume:376 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Gershman Ariel¹^ORCID,Sauria Michael E. G.²^ORCID,Guitart Xavi³^ORCID,Vollger Mitchell R.³^ORCID,Hook Paul W.⁴^ORCID,Hoyt Savannah J.⁵⁶^ORCID,Jain Miten⁷^ORCID,Shumate Alaina⁴^ORCID,Razaghi Roham⁴^ORCID,Koren Sergey⁸^ORCID,Altemose Nicolas⁹^ORCID,Caldas Gina V.¹⁰,Logsdon Glennis A.³^ORCID,Rhie Arang⁸^ORCID,Eichler Evan E.³¹¹^ORCID,Schatz Michael C.²^ORCID,O’Neill Rachel J.⁵⁶^ORCID,Phillippy Adam M.⁸^ORCID,Miga Karen H.⁷^ORCID,Timp Winston¹⁴^ORCID

Affiliation:

1. Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA.

2. Department of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA.

3. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

4. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

5. Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.

6. Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.

7. UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.

8. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

9. Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.

10. Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA, USA.

11. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.

Abstract

The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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