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Son KH, Aldonza MBD, Nam AR, Lee KH, Lee JW, Shin KJ, Kang K, Cho JY. Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. SCIENCE ADVANCES 2023; 9:eade3399. [PMID: 37406108 DOI: 10.1126/sciadv.ade3399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
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Affiliation(s)
- Keun Hong Son
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Mark Borris D Aldonza
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kyung-Ju Shin
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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Pang B, van Weerd JH, Hamoen FL, Snyder MP. Identification of non-coding silencer elements and their regulation of gene expression. Nat Rev Mol Cell Biol 2022; 24:383-395. [DOI: 10.1038/s41580-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
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Zeng W, Liu Q, Yin Q, Jiang R, Wong WH. HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Res 2022; 51:D159-D166. [PMID: 36215037 PMCID: PMC9825415 DOI: 10.1093/nar/gkac859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains ∼262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.
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Affiliation(s)
| | | | | | - Rui Jiang
- Correspondence may also be addressed to Rui Jiang. Tel: +86 10 6279 5578;
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A Missense Variant in the Bardet-Biedl Syndrome 2 Gene ( BBS2) Leads to a Novel Syndromic Retinal Degeneration in the Shetland Sheepdog. Genes (Basel) 2021; 12:genes12111771. [PMID: 34828377 PMCID: PMC8624581 DOI: 10.3390/genes12111771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Canine progressive retinal atrophy (PRA) describes a group of hereditary diseases characterized by photoreceptor cell death in the retina, leading to visual impairment. Despite the identification of multiple PRA-causing variants, extensive heterogeneity of PRA is observed across and within dog breeds, with many still genetically unsolved. This study sought to elucidate the causal variant for a distinct form of PRA in the Shetland sheepdog, using a whole-genome sequencing approach. Filtering variants from a single PRA-affected Shetland sheepdog genome compared to 176 genomes of other breeds identified a single nucleotide variant in exon 11 of the Bardet-Biedl syndrome-2 gene (BBS2) (c.1222G>C; p.Ala408Pro). Genotyping 1386 canids of 155 dog breeds, 15 cross breeds and 8 wolves indicated the c.1222G>C variant was only segregated within Shetland sheepdogs. Out of 505 Shetland sheepdogs, seven were homozygous for the variant. Clinical history and photographs for three homozygotes indicated the presence of a novel phenotype. In addition to PRA, additional clinical features in homozygous dogs support the discovery of a novel syndromic PRA in the breed. The development and utilization of a diagnostic DNA test aim to prevent the mutation from becoming more prevalent in the breed.
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Zeng W, Chen S, Cui X, Chen X, Gao Z, Jiang R. SilencerDB: a comprehensive database of silencers. Nucleic Acids Res 2021; 49:D221-D228. [PMID: 33045745 PMCID: PMC7778955 DOI: 10.1093/nar/gkaa839] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/20/2022] Open
Abstract
Gene regulatory elements, including promoters, enhancers, silencers, etc., control transcriptional programs in a spatiotemporal manner. Though these elements are known to be able to induce either positive or negative transcriptional control, the community has been mostly studying enhancers which amplify transcription initiation, with less emphasis given to silencers which repress gene expression. To facilitate the study of silencers and the investigation of their potential roles in transcriptional control, we developed SilencerDB (http://health.tsinghua.edu.cn/silencerdb/), a comprehensive database of silencers by manually curating silencers from 2300 published articles. The current version, SilencerDB 1.0, contains (1) 33 060 validated silencers from experimental methods, and (ii) 5 045 547 predicted silencers from state-of-the-art machine learning methods. The functionality of SilencerDB includes (a) standardized categorization of silencers in a tree-structured class hierarchy based on species, organ, tissue and cell line and (b) comprehensive annotations of silencers with the nearest gene and potential regulatory genes. SilencerDB, to the best of our knowledge, is the first comprehensive database at this scale dedicated to silencers, with reliable annotations and user-friendly interactive database features. We believe this database has the potential to enable advanced understanding of silencers in regulatory mechanisms and to empower researchers to devise diverse applications of silencers in disease development.
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Affiliation(s)
- Wanwen Zeng
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China.,College of Software, Nankai University, Tianjin 300071, China
| | - Shengquan Chen
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuejian Cui
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaoyang Chen
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zijing Gao
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
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