Complete genomic and epigenetic maps of human centromeres-Reference-Cited by-同舟云学术

Complete genomic and epigenetic maps of human centromeres

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

Author:

Altemose Nicolas¹^ORCID,Logsdon Glennis A.²^ORCID,Bzikadze Andrey V.³^ORCID,Sidhwani Pragya⁴^ORCID,Langley Sasha A.¹,Caldas Gina V.¹,Hoyt Savannah J.⁵⁶^ORCID,Uralsky Lev⁷⁸^ORCID,Ryabov Fedor D.⁹^ORCID,Shew Colin J.¹⁰,Sauria Michael E. G.¹¹^ORCID,Borchers Matthew¹²^ORCID,Gershman Ariel¹³^ORCID,Mikheenko Alla¹⁴,Shepelev Valery A.⁸,Dvorkina Tatiana¹⁴,Kunyavskaya Olga¹⁴^ORCID,Vollger Mitchell R.²^ORCID,Rhie Arang¹⁵^ORCID,McCartney Ann M.¹⁵,Asri Mobin¹⁶,Lorig-Roach Ryan¹⁶^ORCID,Shafin Kishwar¹⁶^ORCID,Lucas Julian K.¹⁶^ORCID,Aganezov Sergey¹⁷^ORCID,Olson Daniel¹⁸^ORCID,de Lima Leonardo Gomes¹²^ORCID,Potapova Tamara¹²^ORCID,Hartley Gabrielle A.⁵⁶,Haukness Marina¹⁶^ORCID,Kerpedjiev Peter¹⁹,Gusev Fedor⁸^ORCID,Tigyi Kristof¹⁶²⁰,Brooks Shelise²¹,Young Alice²¹^ORCID,Nurk Sergey¹⁵^ORCID,Koren Sergey¹⁵^ORCID,Salama Sofie R.¹⁶²⁰^ORCID,Paten Benedict¹⁶²²^ORCID,Rogaev Evgeny I.⁷⁸²³²⁴,Streets Aaron²⁵²⁶^ORCID,Karpen Gary H.¹²⁷^ORCID,Dernburg Abby F.¹²⁰²⁸,Sullivan Beth A.²⁹^ORCID,Straight Aaron F.⁴^ORCID,Wheeler Travis J.¹⁸^ORCID,Gerton Jennifer L.¹²³⁰^ORCID,Eichler Evan E.²²⁰^ORCID,Phillippy Adam M.¹⁵^ORCID,Timp Winston¹³³¹^ORCID,Dennis Megan Y.¹⁰^ORCID,O’Neill Rachel J.⁵⁶^ORCID,Zook Justin M.³²^ORCID,Schatz Michael C.¹⁷^ORCID,Pevzner Pavel A.³³^ORCID,Diekhans Mark¹⁶^ORCID,Langley Charles H.³⁴,Alexandrov Ivan A.⁸¹⁴³⁵^ORCID,Miga Karen H.¹⁶²²^ORCID

Affiliation:

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

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

3. Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA.

4. Department of Biochemistry, Stanford University, Stanford, CA, 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. Sirius University of Science and Technology, Sochi, Russia.

8. Vavilov Institute of General Genetics, Moscow, Russia.

9. Moscow Polytechnic University, Moscow, Russia.

10. Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.

11. Department of Biology, Johns Hopkins University, Baltimore, MD, USA.

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

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

14. Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia.

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

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

17. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

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

19. Reservoir Genomics, Oakland, CA.

20. Howard Hughes Medical Institute, Chevy Chase, MD, USA.

21. NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

22. Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA.

23. Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA.

24. Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.

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

26. Chan Zuckerberg Biohub, San Francisco, CA, USA.

27. BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

28. Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.

29. Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.

30. University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA.

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

32. Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.

33. Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA.

34. Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.

35. Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

Abstract

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference154 articles.

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