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Li Z, Schlick T. Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res 2024; 52:583-599. [PMID: 38015443 PMCID: PMC10810283 DOI: 10.1093/nar/gkad1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
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3
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Zhang Y, Gao H, Li H, Guo J, Ouyang B, Wang M, Xu Q, Wang J, Lv M, Guo X, Liu Q, Wei L, Ren H, Xi Y, Guo Y, Ren B, Pan S, Liu C, Ding X, Xiang H, Yu Y, Song Y, Meng L, Liu S, Wang J, Jiang Y, Shi J, Liu S, Sabir JS, Sabir MJ, Khan M, Hajrah NH, Ming-Yuen Lee S, Xu X, Yang H, Wang J, Fan G, Yang N, Liu X. The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish. iScience 2020; 23:101754. [PMID: 33251490 PMCID: PMC7677710 DOI: 10.1016/j.isci.2020.101754] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/17/2020] [Accepted: 10/28/2020] [Indexed: 01/27/2023] Open
Abstract
Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies.
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Affiliation(s)
- Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Haoyang Gao
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jiao Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Bingjie Ouyang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Meiniang Wang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Qiwu Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jiahao Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Meiqi Lv
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xinyu Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Likun Wei
- City University of Hongkong, Kowloon, Hongkong SAR
| | - Han Ren
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yang Xi
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yang Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Bingzhao Ren
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chuxin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiaoyan Ding
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yingjia Yu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lingfeng Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jun Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yuan Jiang
- BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics, Inc., San Jose, CA 95134, USA
| | - Jiahai Shi
- City University of Hongkong, Kowloon, Hongkong SAR
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jamal S.M. Sabir
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Mumdooh J. Sabir
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Muhummadh Khan
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Nahid H. Hajrah
- Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics, Inc., San Jose, CA 95134, USA
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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Matsunami M, Suzuki M, Haramoto Y, Fukui A, Inoue T, Yamaguchi K, Uchiyama I, Mori K, Tashiro K, Ito Y, Takeuchi T, Suzuki KIT, Agata K, Shigenobu S, Hayashi T. A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. DNA Res 2019; 26:217-229. [PMID: 31006799 PMCID: PMC6589553 DOI: 10.1093/dnares/dsz003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic and genome editing methods. However, limited genetic information is available for P. waltl. We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. We generated 1.2 billion Illumina reads from a wide variety of samples across 12 different tissues/organs, unfertilized egg, and embryos at eight different developmental stages. These reads were assembled into 1,395,387 contigs, from which 202,788 non-redundant ORF models were constructed. The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Our transcriptome resource is expected to enhance future research employing this emerging model animal for regeneration research as well as for investigations in other areas including developmental biology, stem cell biology, and cancer research. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).
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Affiliation(s)
- Masatoshi Matsunami
- Department of Advanced Genomics and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Okinawa, Japan
| | - Miyuki Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Akimasa Fukui
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-Ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ikuo Uchiyama
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazuki Mori
- Computational Bio Big-Data Open Innovation Lab. (CBBD-OIL), Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Shinjuku-Ku, Tokyo, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Takeuchi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Ken-ichi T Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
- Center for the Development of New Model Organisms, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Toshinori Hayashi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
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