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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
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Hoencamp, Claire [1] ; Dudchenko, Olga [2, 3, 4] ; Elbatsh, Ahmed M. O. [1, 5] ; Brahmachari, Sumitabha [2] ; Raaijmakers, Jonne A. [6] ; van Schaik, Tom [7] ; Cacciatore, Angela Sedeno [1] ; Contessoto, Vinicius G. [2, 8] ; van Heesbeen, Roy G. H. P. [6, 9] ; van den Broek, Bram [10] ; Mhaskar, Aditya N. [1, 11] ; Teunissen, Hans [7] ; St Hilaire, Brian Glenn [3, 4] ; Weisz, David [3, 4] ; Omer, Arina D. [4] ; Pham, Melanie [4] ; Colaric, Zane [4] ; Yang, Zhenzhen [12] ; Rao, Suhas S. P. [3, 4, 13] ; Mitra, Namita [3, 4] ; Lui, Christopher [4] ; Yao, Weijie [4] ; Khan, Ruqayya [3, 4] ; Moroz, Leonid L. [14, 15] ; Kohn, Andrea [14, 15] ; St Leger, Judy [16] ; Mena, Alexandria [17] ; Holcroft, Karen [18] ; Gambetta, Maria Cristina [19] ; Lim, Fabian [20] ; Farley, Emma [20] ; Stein, Nils [21, 22, 23] ; Haddad, Alexander [4] ; Chauss, Daniel [24] ; Mutlu, Ayse Sena [3] ; Wang, Meng C. [3, 25, 26] ; Young, Neil D. [27] ; Hildebrandt, Evin [28, 29] ; Cheng, Hans H. [28] ; Knight, Christopher J. [30] ; Burnham, Theresa L. U. [31, 32, 33] ; Hovel, Kevin A. [32, 33] ; Beel, Andrew J. [13] ; Mattei, Pierre-Jean [13] ; Kornberg, Roger D. [13] ; Warren, Wesley C. [34] ; Cary, Gregory [35] ; Gomez-Skarmeta, Jose Luis [36] ; Hinman, Veronica [37] ; Lindblad-Toh, Kerstin [38, 39] ; Di Palma, Federica [40] ; Maeshima, Kazuhiro [41, 42] ; Multani, Asha S. [43] ; Pathak, Sen ; Nel-Themaat, Liesl [44, 45] ; Behringer, Richard R. [44] ; Kaur, Parwinder [21] ; Medema, Rene H. [6] ; van Steensel, Bas [7] ; de Wit, Elzo [7] ; Onuchic, Jose N. [46, 2, 47, 48] ; Di Pierro, Michele [2, 49] ; Aiden, Erez Lieberman [2, 38, 3, 4, 12, 21] ; Rowland, Benjamin D. [1]
Total Authors: 64
Affiliation:
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[1] Netherlands Canc Inst, Div Gene Regulat, NL-1066 CX Amsterdam - Netherlands
[2] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 - USA
[3] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 - USA
[4] Baylor Coll Med, Ctr Genome Architecture, Houston, TX 77030 - USA
[5] Novartis Inst Biomed Res, CH-4002 Basel - Switzerland
[6] Netherlands Canc Inst, Oncode Inst, Div Cell Biol, NL-1066 CX Amsterdam - Netherlands
[7] Netherlands Canc Inst, Oncode Inst, Div Gene Regulat, NL-1066 CX Amsterdam - Netherlands
[8] Sao Paulo State Univ UNESP, Inst Biosci Letters & Exact Sci, Dept Phys, BR-15054000 Sao Jose Do Rio Preto, SP - Brazil
[9] Janssen Vaccines & Prevent BV, NL-2333 CN Leiden - Netherlands
[10] Netherlands Canc Inst, BioImaging Facil, NL-1066 CX Amsterdam - Netherlands
[11] Univ Med Ctr Rotterdam, Erasmus MC, Dept Dev Biol, NL-3015 GD Rotterdam - Netherlands
[12] ShanghaiTech, Shanghai Inst Adv Immunochem Studies, Pudong 201210 - Peoples R China
[13] Stanford Univ, Dept Struct Biol, Sch Med, Stanford, CA 94305 - USA
[14] Univ Florida, Whitney Lab, Gainesville, FL 32611 - USA
[15] Univ Florida, Dept Neurosci, Gainesville, FL 32611 - USA
[16] Cornell Univ, Dept Biosci, Coll Vet Med, Ithaca, NY 14853 - USA
[17] SeaWorld San Diego, San Diego, CA 92109 - USA
[18] Moody Gardens, Galveston, TX 77554 - USA
[19] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne - Switzerland
[20] Univ Calif San Diego, Dept Med & Mol Biol, La Jolla, CA 92093 - USA
[21] Univ Western Australia, UWA Sch Agr & Environm, Perth, WA 6009 - Australia
[22] Leibniz Inst Plant Genet & Crop Plant Res IPK Gat, D-06466 Seeland - Germany
[23] Georg August Univ Gottingen, Ctr Integrated Breeding Res CiBreed, Dept Crop Sci, D-37075 Gottingen - Germany
[24] NIDDK, NIH, Bethesda, MD 20892 - USA
[25] Baylor Coll Med, Huffington Ctr Aging, Houston, TX 77030 - USA
[26] Baylor Coll Med, Howard Hughes Med Inst, Houston, TX 77030 - USA
[27] Univ Melbourne, Fac Vet & Agr Sci, Parkville, Vic 3010 - Australia
[28] ARS, Avian Dis & Oncol Lab, USDA, E Lansing, MI 48823 - USA
[29] Zoetis, VMRD Global Biol Res, Kalamazoo, MI 49007 - USA
[30] Stanford Univ, Hopkins Marine Stn, Pacific Grove, CA 93950 - USA
[31] Univ Calif Davis, Dept Wildlife Fish & Conservat Biol, Davis, CA 95616 - USA
[32] San Diego State Univ, Coastal & Marine Inst, San Diego, CA 92106 - USA
[33] San Diego State Univ, Dept Biol, San Diego, CA 92106 - USA
[34] Univ Missouri, Dept Anim Sci, Columbia, MO 65211 - USA
[35] Jackson Lab, Bar Harbor, ME 04609 - USA
[36] Univ Pablo de Olavide, Ctr Andaluz Biol Desarrollo, CSIC, Seville 41013 - Spain
[37] Carnegie Mellon Univ, Dept Biol Sci, Pittsburgh, PA 15213 - USA
[38] Broad Inst MIT & Harvard, Cambridge, MA 02142 - USA
[39] Uppsala Univ, Dept Med Biochem & Microbiol, Sci Life Lab, S-75123 Uppsala - Sweden
[40] Univ East Anglia, Dept Biol Sci, Norwich NR4 7TJ, Norfolk - England
[41] Natl Inst Genet, Genome Dynam Lab, Mishima, Shizuoka 4118540 - Japan
[42] Sokendai Grad Univ Adv Studies, Dept Genet, Mishima, Shizuoka 4118540 - Japan
[43] Univ Texas MD Anderson Canc Ctr, Dept Genet, Houston, TX 77030 - USA
[44] Sen Pathak, Univ Texas MD Anderson Canc Ctr, Dept Genet, Houston, TX 77030 - USA
[45] Univ Colorado Adv Reprod Med, Denver, CO 80238 - USA
[46] Rice Univ, Dept Chem, Houston, TX 77005 - USA
[47] Rice Univ, Dept Biosci, Houston, TX 77005 - USA
[48] Rice Univ, Dept Phys & Astron, Houston, TX 77005 - USA
[49] Northeastern Univ, Dept Phys, Boston, MA 02115 - USA
Total Affiliations: 49
Document type: Journal article
Source: Science; v. 372, n. 6545, p. 984+, MAY 28 2021.
Web of Science Citations: 1
Abstract

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes. (AU)

FAPESP's process: 16/13998-8 - Rational evolution by computational methods applied to predict mutations in enzymes to biofuels production
Grantee:Vinícius de Godoi Contessoto
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production
Grantee:Vinícius de Godoi Contessoto
Support Opportunities: Scholarships abroad - Research Internship - Post-doctor