3D genomics across the tree of life reveals condensin II as a determinant of architecture type-Reference-Cited by-同舟云学术

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Published:2021-05-28 Issue:6545 Volume:372 Page:984-989
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Hoencamp Claire¹^ORCID,Dudchenko Olga²³⁴^ORCID,Elbatsh Ahmed M. O.¹^ORCID,Brahmachari Sumitabha⁴^ORCID,Raaijmakers Jonne A.⁵^ORCID,van Schaik Tom⁶^ORCID,Sedeño Cacciatore Ángela¹^ORCID,Contessoto Vinícius G.⁴⁷^ORCID,van Heesbeen Roy G. H. P.⁵,van den Broek Bram⁸^ORCID,Mhaskar Aditya N.¹^ORCID,Teunissen Hans⁶,St Hilaire Brian Glenn²³,Weisz David²³^ORCID,Omer Arina D.²^ORCID,Pham Melanie²^ORCID,Colaric Zane²,Yang Zhenzhen⁹,Rao Suhas S. P.²³¹⁰,Mitra Namita²³,Lui Christopher²^ORCID,Yao Weijie²,Khan Ruqayya²³^ORCID,Moroz Leonid L.¹¹^ORCID,Kohn Andrea¹¹,St. Leger Judy¹²^ORCID,Mena Alexandria¹³,Holcroft Karen¹⁴,Gambetta Maria Cristina¹⁵^ORCID,Lim Fabian¹⁶^ORCID,Farley Emma¹⁶^ORCID,Stein Nils¹⁷¹⁸¹⁹^ORCID,Haddad Alexander²,Chauss Daniel²⁰,Mutlu Ayse Sena³^ORCID,Wang Meng C.³²¹²²^ORCID,Young Neil D.²³^ORCID,Hildebrandt Evin²⁴^ORCID,Cheng Hans H.²⁴^ORCID,Knight Christopher J.²⁵^ORCID,Burnham Theresa L. U.²⁶²⁷^ORCID,Hovel Kevin A.²⁷^ORCID,Beel Andrew J.¹⁰^ORCID,Mattei Pierre-Jean¹⁰,Kornberg Roger D.¹⁰^ORCID,Warren Wesley C.²⁸^ORCID,Cary Gregory²⁹^ORCID,Gómez-Skarmeta José Luis³⁰,Hinman Veronica³¹^ORCID,Lindblad-Toh Kerstin³²³³^ORCID,Di Palma Federica³⁴,Maeshima Kazuhiro³⁵³⁶^ORCID,Multani Asha S.³⁷^ORCID,Pathak Sen³⁷^ORCID,Nel-Themaat Liesl³⁷,Behringer Richard R.³⁷,Kaur Parwinder¹⁹^ORCID,Medema René H.⁵,van Steensel Bas⁶^ORCID,de Wit Elzo⁶^ORCID,Onuchic José N.⁴³⁸^ORCID,Di Pierro Michele⁴³⁹^ORCID,Lieberman Aiden Erez²³⁴⁹¹⁹^ORCID,Rowland Benjamin D.¹^ORCID

Affiliation:

1. Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.

2. The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

3. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

4. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.

5. Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.

6. Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.

7. Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto – SP, 15054-000, Brazil.

8. BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.

9. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China.

10. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

11. Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA.

12. Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA.

13. SeaWorld San Diego, San Diego, CA 92109, USA.

14. Moody Gardens, Galveston, TX 77554, USA.

15. Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.

16. Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.

17. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany.

18. Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany.

19. UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.

20. National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

21. Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA.

22. Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.

23. Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia.

24. Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA.

25. Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.

26. Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA.

27. Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA.

28. Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.

29. The Jackson Laboratory, Bar Harbor, ME 04609, USA.

30. Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain.

31. Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

32. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

33. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden.

34. Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

35. Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.

36. Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.

37. Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

38. Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA.

39. Department of Physics, Northeastern University, Boston, MA 02115, USA.

Abstract

Organismal evolution of the 3D genome The conformation of chromosomes within the nucleus can reflect a cell's type or state. However, studies of the conservation and evolutionary history of the mechanisms regulating genome structure across species are lacking. Hoencamp et al. mapped three-dimensional (3D) genome organization in 24 eukaryote species, including animals, fungi, and plants. At interphase, species' telomeres and centromeres either clustered across chromosomes or oriented in a polarized state maintaining individual chromosomal territories within the cell, a difference attributed to condensin II. An experimental loss of condensin II in human cells promotes the formation of centromere clusters but has no effect on loop or compartment formation. Whether the structure of the 3D genome varies across species may thus depend on whether they carry a functional condensin II gene. Science , abe2218, this issue p. 984

Funder

National Science Foundation

National Institutes of Health

Howard Hughes Medical Institute

European Research Council

Ministerio de Economía y Competitividad

U.S. Department of Agriculture

Welch Foundation

Boehringer Ingelheim Fonds

Nederlandse Organisatie voor Wetenschappelijk Onderzoek

The University of Western Australia

Australian Government