한빛사논문
- 조회1,085
Marta Farré1,*, Jaebum Kim2,*, Anastasia A. Proskuryakova3,4, Yang Zhang5, Anastasia I. Kulemzina3, Qiye Li6, Yang Zhou6, Yingqi Xiong6, Jennifer L. Johnson7, Polina Perelman3,4, Warren E. Johnson8,9, Wesley C. Warren10, Anna V. Kukekova7, Guojie Zhang6,11,12, Stephen J. O’Brien13, Oliver A. Ryder14, Alexander S. Graphodatsky3,4, Jian Ma5, Harris A. Lewin15, Denis M. Larkin1,16
1 Royal Veterinary College, University of London, London NW1 0TU, UK.
2 Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea.
3 Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.
4 Novosibirsk State University, Novosibirsk 630090, Russia.
5 Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
6 China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.
7 Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
8 Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA.
9 Walter Reed Biosystematics Unit, Museum Support Center, Smithsonian Institution, 4210 Silver Hill Rd., Suitland MD 20746, USA.
10 Bond Life Sciences Center, University of Missouri, 1202 Rollins St., Columbia, MO 63201, USA.
11 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
12 Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
13 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.
14 Institute for Conservation Research, San Diego Zoo, Escondido, CA 92027, USA.
15 Department of Evolution and Ecology, and the UC Davis Genome Center, University of California, Davis, CA 95616, USA.
16 The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia.
* These authors contributed equally to this work.
Corresponding author: Denis M. Larkin
Abstract
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls, was characterized by mostly intrachromosomal changes while the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. Notably, this divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements co-localized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.
논문정보
- Research article
- 2019년 02월 (BRIC 등록일 2019-02-27)
- 국내+국외 연구진
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