研究者データベース
Last Updated :2024/08/07
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鍾, チョン名
奕洛, イェキロク（クレア）ID各種
202201006914603233
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論文
- Osamu Iwasaki, Sanki Tashiro, Claire Chung, Tomomi Hayashi, Hideki Tanizawa, Xuebing Wang, Shinya Ohta, Yuko Fujioka, Joseph Han, Gabrielle Tabor, Mikihiro Kawagoe, Ronen Marmorstein, Nobuo N Noda, Ken-Ichi NomabioRxiv : the preprint server for biology 2024年06月28日Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensinmediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation.
- Xuebing Wang, Claire Yik-Lok Chung, Ai Yoshioka, Shinya Hashimoto, Haruki Jimbo, Hideki Tanizawa, Shinya Ohta, Takeshi Fukumoto, Ken-ichi NomaJournal of Investigative Dermatology 2024年04月 [査読有り][通常論文]
- Le Li, Chenyang Hong, Jie Xu, Claire Yik-Lok Chung, Alden King-Yung Leung, Delbert Almerick T Boncan, Lixin Cheng, Kwok-Wai Lo, Paul B S Lai, John Wong, Jingying Zhou, Alfred Sze-Lok Cheng, Ting-Fung Chan, Feng Yue, Kevin Y YipBriefings in Bioinformatics 25 1 2023年11月22日 [査読有り][通常論文]
Abstract Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample. - Hongbo Wang, Hin Ting Wan, Bin Wu, Jianbo Jian, Alice H M Ng, Claire Yik-Lok Chung, Eugene Yui-Ching Chow, Jizhou Zhang, Anderson O L Wong, Keng Po Lai, Ting Fung Chan, Eric Lu Zhang, Chris Kong-Chu WongGigaScience 2022年12月08日 [査読有り][通常論文]
- Wang, X., Li, M.-W., Wong, F.-L., Luk, C.-Y., Chung, C.Y.-L., Yung, W.-S., Wang, Z., Xie, M., Song, S., Chung, G., Chan, T.-F., Lam, H.-M.Plant Journal 107 6 2021年07月10日 [査読有り]
- K. Shirasawa, C. Chung, D. Boncan, H. Hirakawa, F. Maeda, T. Wada, T.F. Chan, S. IsobeActa Horticulturae 1309 1309 175 - 180 2021年04月 [査読有り]
Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, which chromosome number is 2n=8x=56. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese cultivar. Genomes of diploid Fragaria species were re-sequenced and compared with the most similar chromosome-scale scaffolds to investigate possible progenitor of each subgenomes. The Illumina short reads derived from paired-end, mate pair and 10X Genomics libraries were obtained from a Japanese cultivar, 'Reikou'. The scafffolds assembled using Denovo MAGIC 3.0 consisted of 32,715 sequences with a total length of 1.4 Gb and N50 length of 3.9 Mb. The scaffolds were aligned onto the 'Reikou' S1 linkage maps with IStraw90 Axiom SaNP array and ddRAD-Seq for pseudomolecule construction. - Wei Li, Claire Yik Lok Chung, Chi Chiu Wang, Ting Fung Chan, Maran Bo Wah Leung, Oi Ka Chan, Ling Wu, Kubi Appiah, Piya Chaemsaithong, Yvonne Kwun Yue Cheng, Liona Chiu Yee Poon, Tak Yeung LeungAmerican Journal of Obstetrics and Gynecology 223 5 749.e1 - 749.e16 2020年11月 [査読有り][通常論文]
- Yuan, Y., Chung, C.Y.-L., Chan, T.-F.Computational and Structural Biotechnology Journal 18 2051 - 2062 2020年08月01日 [査読有り]
- Sachiko Isobe, Yuki Matsumoto, Claire Chung, Mika Sakamoto, Ting-Fung Chan, Hideki Hirakawa, Genki Ishihara, Hon-Ming Lam, Shinobu Nakayama, Shigemi Sasamoto, Yasuhiro Tanizawa, Akiko Watanabe, Kei Watanabe, Masaru Yagura, Yasukazu NakamurabioRxiv 2020年05月19日 [査読無し][通常論文]
Abstract The domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat, Felis catus genome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and ab initio gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care. - Babu Valliyodan, Steven B. Cannon, Philipp E. Bayer, Shengqiang Shu, Anne V. Brown, Longhui Ren, Jerry Jenkins, Claire Y.‐L. Chung, Ting‐Fung Chan, Christopher G. Daum, Christopher Plott, Alex Hastie, Kobi Baruch, Kerrie W. Barry, Wei Huang, Gunvant Patil, Rajeev K. Varshney, Haifei Hu, Jacqueline Batley, Yuxuan Yuan, Qijian Song, Robert M. Stupar, David M. Goodstein, Gary Stacey, Hon‐Ming Lam, Scott A. Jackson, Jeremy Schmutz, Jane Grimwood, David Edwards, Henry T. NguyenThe Plant Journal 100 5 1066 - 1082 2019年10月28日 [査読有り][通常論文]
Summary We report reference‐quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species. - Min Xie, Claire Yik-Lok Chung, Man-Wah Li, Fuk-Ling Wong, Xin Wang, Ailin Liu, Zhili Wang, Alden King-Yung Leung, Tin-Hang Wong, Suk-Wah Tong, Zhixia Xiao, Kejing Fan, Ming-Sin Ng, Xinpeng Qi, Linfeng Yang, Tianquan Deng, Lijuan He, Lu Chen, Aisi Fu, Qiong Ding, Junxian He, Gyuhwa Chung, Sachiko Isobe, Takanari Tanabata, Babu Valliyodan, Henry T. Nguyen, Steven B. Cannon, Christine H. Foyer, Ting-Fung Chan, Hon-Ming LamNature Communications 10 1 2019年03月14日 [査読有り][通常論文]
- Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, Le Li, Alden K. Y. Leung, Jennifer McCaffrey, Eleanor Young, Ernest T. Lam, Alex R. Hastie, Karen H. Y. Wong, Claire Y. L. Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene Y. C. Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao, Pui-Yan KwokNature Communications 10 1 2019年03月04日 [査読有り][通常論文]
Abstract Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome. - CHIM, Siu Chung Stephen, WONG, Ka Wing Karen, CHUNG, Yik Lok, LAM, Ka Wai, KWOK, Sui Lam, LAI, Chit Ying, CHENG, Kwun Yue Yvonne, CHAN, Oi Ka Catherine, TSUI, Kwok Wing, CHAN, Ting Fung Philos, LEUNG, Tak YeungInternational Journal of Molecular Sciences 18 1709 - 1709 2017年08月 [査読有り][通常論文]
書籍等出版物
- Yim, Aldrin, Chung, Claire, Yu, Allen
Packt Publishing 2018年 (ISBN: 9781788625173) v, 287 p. - Allen Yu, Claire Chung, Aldrin Yim
Packt Publishing 2017年08月 (ISBN: 1788295269) 334
講演・口頭発表等
- オプティカルゲノムマッピングによる大規模ゲノム構造反復の検測 [通常講演]鍾 奕洛, 陳 廷峰日本遺伝学会第94回大会 口頭発表（一般）
- Claire Chung第44回日本分子生物学会年会 2021年12月 ポスター発表
- Pan-genome Analysis of Wild;cultivated Soybean Germplasms to Investigate Large Genomics Structural Variations [招待講演]International Meeting on Multiomics Platform Dvelopment cum AoE Symposium 口頭発表（招待・特別）
- Multiple Alignment of Optical Mapping Facilitates Typing in Complex RegionsClaire Yik-Lok Chung, Alden King-Yung Leung, Ting-Fung ChanInternational Plant & Animal Genome (PAG) XXV ポスター発表