From telomere to telomere: The transcriptional and epigenetic state of human repeat elements-Reference-Cited by-同舟云学术

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

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

Author:

Hoyt Savannah J.¹^ORCID,Storer Jessica M.²^ORCID,Hartley Gabrielle A.¹,Grady Patrick G. S.¹^ORCID,Gershman Ariel³^ORCID,de Lima Leonardo G.⁴^ORCID,Limouse Charles⁵,Halabian Reza⁶^ORCID,Wojenski Luke¹^ORCID,Rodriguez Matias⁶^ORCID,Altemose Nicolas⁷^ORCID,Rhie Arang⁸^ORCID,Core Leighton J.¹⁹^ORCID,Gerton Jennifer L.⁴^ORCID,Makalowski Wojciech⁶^ORCID,Olson Daniel¹⁰^ORCID,Rosen Jeb²^ORCID,Smit Arian F. A.²^ORCID,Straight Aaron F.⁵^ORCID,Vollger Mitchell R.¹¹^ORCID,Wheeler Travis J.¹⁰^ORCID,Schatz Michael C.¹²^ORCID,Eichler Evan E.¹¹¹³^ORCID,Phillippy Adam M.⁸^ORCID,Timp Winston³¹⁴^ORCID,Miga Karen H.¹⁵^ORCID,O’Neill Rachel J.¹⁹¹⁶^ORCID

Affiliation:

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

2. Institute for Systems Biology, Seattle, WA, USA.

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

4. Stowers Institute for Medical Research, Kansas City, MO, USA.

5. Department of Biochemistry, Stanford University, Stanford, CA, USA.

6. Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany.

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

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

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

10. Department of Computer Science, University of Montana, Missoula, MT, USA.

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

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

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

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

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

16. Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.

Abstract

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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