Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-10DOI: 10.1016/j.xgen.2024.100606
Katelyn R Titus, Zoltan Simandi, Harshini Chandrashekar, Dominik Paquet, Jennifer E Phillips-Cremins
{"title":"Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.","authors":"Katelyn R Titus, Zoltan Simandi, Harshini Chandrashekar, Dominik Paquet, Jennifer E Phillips-Cremins","doi":"10.1016/j.xgen.2024.100606","DOIUrl":"10.1016/j.xgen.2024.100606","url":null,"abstract":"<p><p>DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100606"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Crosstalk between epitranscriptomic and epigenomic modifications and its implication in human diseases.","authors":"Chengyu Li, Kexuan Chen, Qianchen Fang, Shaohui Shi, Jiuhong Nan, Jialin He, Yafei Yin, Xiaoyu Li, Jingyun Li, Lei Hou, Xinyang Hu, Manolis Kellis, Xikun Han, Xushen Xiong","doi":"10.1016/j.xgen.2024.100605","DOIUrl":"10.1016/j.xgen.2024.100605","url":null,"abstract":"<p><p>Crosstalk between N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) and epigenomes is crucial for gene regulation, but its regulatory directionality and disease significance remain unclear. Here, we utilize quantitative trait loci (QTLs) as genetic instruments to delineate directional maps of crosstalk between m<sup>6</sup>A and two epigenomic traits, DNA methylation (DNAme) and H3K27ac. We identify 47 m<sup>6</sup>A-to-H3K27ac and 4,733 m<sup>6</sup>A-to-DNAme and, in the reverse direction, 106 H3K27ac-to-m<sup>6</sup>A and 61,775 DNAme-to-m<sup>6</sup>A regulatory loci, with differential genomic location preference observed for different regulatory directions. Integrating these maps with complex diseases, we prioritize 20 genome-wide association study (GWAS) loci for neuroticism, depression, and narcolepsy in brain; 1,767 variants for asthma and expiratory flow traits in lung; and 249 for coronary artery disease, blood pressure, and pulse rate in muscle. This study establishes disease regulatory paths, such as rs3768410-DNAme-m<sup>6</sup>A-asthma and rs56104944-m<sup>6</sup>A-DNAme-hypertension, uncovering locus-specific crosstalk between m<sup>6</sup>A and epigenomic layers and offering insights into regulatory circuits underlying human diseases.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100605"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-30DOI: 10.1016/j.xgen.2024.100626
Shenghan Gao, Yanyan Jia, Hongtao Guo, Tun Xu, Bo Wang, Stephen J Bush, Shijie Wan, Yimeng Zhang, Xiaofei Yang, Kai Ye
{"title":"The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.","authors":"Shenghan Gao, Yanyan Jia, Hongtao Guo, Tun Xu, Bo Wang, Stephen J Bush, Shijie Wan, Yimeng Zhang, Xiaofei Yang, Kai Ye","doi":"10.1016/j.xgen.2024.100626","DOIUrl":"10.1016/j.xgen.2024.100626","url":null,"abstract":"<p><p>Understanding the roles played by centromeres in chromosome evolution and speciation is complicated by the fact that centromeres comprise large arrays of tandemly repeated satellite DNA, which hinders high-quality assembly. Here, we used long-read sequencing to generate nearly complete genome assemblies for four karyotypically diverse Papaver species, P. setigerum (2n = 44), P. somniferum (2n = 22), P. rhoeas (2n = 14), and P. bracteatum (2n = 14), collectively representing 45 gapless centromeres. We identified four centromere satellite (cenSat) families and experimentally validated two representatives. For the two allopolyploid genomes (P. somniferum and P. setigerum), we characterized the subgenomic distribution of each satellite and identified a \"homogenizing\" phase of centromere evolution in the aftermath of hybridization. An interspecies comparison of the peri-centromeric regions further revealed extensive centromere-mediated chromosome rearrangements. Taking these results together, we propose a model for studying cenSat competition after hybridization and shed further light on the complex role of the centromere in speciation.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100626"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-11DOI: 10.1016/j.xgen.2024.100607
Jiahong Wu, Fujiang Liu, Jie Jiao, Haoran Luo, Shiyu Fan, Jiao Liu, Hongxiang Wang, Ning Cui, Ning Zhao, Qingming Qu, Shigehiro Kuraku, Zhen Huang, Luohao Xu
{"title":"Comparative genomics illuminates karyotype and sex chromosome evolution of sharks.","authors":"Jiahong Wu, Fujiang Liu, Jie Jiao, Haoran Luo, Shiyu Fan, Jiao Liu, Hongxiang Wang, Ning Cui, Ning Zhao, Qingming Qu, Shigehiro Kuraku, Zhen Huang, Luohao Xu","doi":"10.1016/j.xgen.2024.100607","DOIUrl":"10.1016/j.xgen.2024.100607","url":null,"abstract":"<p><p>Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100607"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-30DOI: 10.1016/j.xgen.2024.100625
Yoshihiko Tomofuji, Ryuya Edahiro, Kyuto Sonehara, Yuya Shirai, Kian Hong Kock, Qingbo S Wang, Shinichi Namba, Jonathan Moody, Yoshinari Ando, Akari Suzuki, Tomohiro Yata, Kotaro Ogawa, Tatsuhiko Naito, Ho Namkoong, Quy Xiao Xuan Lin, Eliora Violain Buyamin, Le Min Tan, Radhika Sonthalia, Kyung Yeon Han, Hiromu Tanaka, Ho Lee, Tatsusada Okuno, Boxiang Liu, Koichi Matsuda, Koichi Fukunaga, Hideki Mochizuki, Woong-Yang Park, Kazuhiko Yamamoto, Chung-Chau Hon, Jay W Shin, Shyam Prabhakar, Atsushi Kumanogoh, Yukinori Okada
{"title":"Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.","authors":"Yoshihiko Tomofuji, Ryuya Edahiro, Kyuto Sonehara, Yuya Shirai, Kian Hong Kock, Qingbo S Wang, Shinichi Namba, Jonathan Moody, Yoshinari Ando, Akari Suzuki, Tomohiro Yata, Kotaro Ogawa, Tatsuhiko Naito, Ho Namkoong, Quy Xiao Xuan Lin, Eliora Violain Buyamin, Le Min Tan, Radhika Sonthalia, Kyung Yeon Han, Hiromu Tanaka, Ho Lee, Tatsusada Okuno, Boxiang Liu, Koichi Matsuda, Koichi Fukunaga, Hideki Mochizuki, Woong-Yang Park, Kazuhiko Yamamoto, Chung-Chau Hon, Jay W Shin, Shyam Prabhakar, Atsushi Kumanogoh, Yukinori Okada","doi":"10.1016/j.xgen.2024.100625","DOIUrl":"10.1016/j.xgen.2024.100625","url":null,"abstract":"<p><p>Several X-linked genes escape from X chromosome inactivation (XCI), while differences in escape across cell types and tissues are still poorly characterized. Here, we developed scLinaX for directly quantifying relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA sequencing (scRNA-seq) data. The scLinaX and differentially expressed gene analyses with large-scale blood scRNA-seq datasets consistently identified the stronger escape in lymphocytes than in myeloid cells. An extension of scLinaX to a 10x multiome dataset (scLinaX-multi) suggested a stronger escape in lymphocytes than in myeloid cells at the chromatin-accessibility level. The scLinaX analysis of human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes suggested the underlying impact of escape on the genotype-phenotype association. Overall, scLinaX and the quantified escape catalog identified the heterogeneity of escape across cell types and tissues.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100625"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406184/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-24DOI: 10.1016/j.xgen.2024.100610
Yuki Sugiyama, Satoshi Okada, Yasukazu Daigaku, Emiko Kusumoto, Takashi Ito
{"title":"Strategic targeting of Cas9 nickase induces large segmental duplications.","authors":"Yuki Sugiyama, Satoshi Okada, Yasukazu Daigaku, Emiko Kusumoto, Takashi Ito","doi":"10.1016/j.xgen.2024.100610","DOIUrl":"10.1016/j.xgen.2024.100610","url":null,"abstract":"<p><p>Gene/segmental duplications play crucial roles in genome evolution and variation. Here, we introduce paired nicking-induced amplification (PNAmp) for their experimental induction. PNAmp strategically places two Cas9 nickases upstream and downstream of a replication origin on opposite strands. This configuration directs the sister replication forks initiated from the origin to break at the nicks, generating a pair of one-ended double-strand breaks. If homologous sequences flank the two break sites, then end resection converts them to single-stranded DNAs that readily anneal to drive duplication of the region bounded by the homologous sequences. PNAmp induces duplication of segments as large as ∼1 Mb with efficiencies exceeding 10% in the budding yeast Saccharomyces cerevisiae. Furthermore, appropriate splint DNAs allow PNAmp to duplicate/multiplicate even segments not bounded by homologous sequences. We also provide evidence for PNAmp in mammalian cells. Therefore, PNAmp provides a prototype method to induce structural variations by manipulating replication fork progression.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100610"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141763060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-08-02DOI: 10.1016/j.xgen.2024.100627
Jayne A Barbour, Tong Ou, Haocheng Yang, Hu Fang, Noel C Yue, Xiaoqiang Zhu, Michelle W Wong-Brown, Yuen T Wong, Nikola A Bowden, Song Wu, Jason W H Wong
{"title":"ERCC2 mutations alter the genomic distribution pattern of somatic mutations and are independently prognostic in bladder cancer.","authors":"Jayne A Barbour, Tong Ou, Haocheng Yang, Hu Fang, Noel C Yue, Xiaoqiang Zhu, Michelle W Wong-Brown, Yuen T Wong, Nikola A Bowden, Song Wu, Jason W H Wong","doi":"10.1016/j.xgen.2024.100627","DOIUrl":"10.1016/j.xgen.2024.100627","url":null,"abstract":"<p><p>Excision repair cross-complementation group 2 (ERCC2) encodes the DNA helicase xeroderma pigmentosum group D, which functions in transcription and nucleotide excision repair. Point mutations in ERCC2 are putative drivers in around 10% of bladder cancers (BLCAs) and a potential positive biomarker for cisplatin therapy response. Nevertheless, the prognostic significance directly attributed to ERCC2 mutations and its pathogenic role in genome instability remain poorly understood. We first demonstrated that mutant ERCC2 is an independent predictor of prognosis in BLCA. We then examined its impact on the somatic mutational landscape using a cohort of ERCC2 wild-type (n = 343) and mutant (n = 39) BLCA whole genomes. The genome-wide distribution of somatic mutations is significantly altered in ERCC2 mutants, including T[C>T]N enrichment, altered replication time correlations, and CTCF-cohesin binding site mutation hotspots. We leverage these alterations to develop a machine learning model for predicting pathogenic ERCC2 mutations, which may be useful to inform treatment of patients with BLCA.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100627"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-16DOI: 10.1016/j.xgen.2024.100609
Taehwan Shin, Janet H T Song, Michael Kosicki, Connor Kenny, Samantha G Beck, Lily Kelley, Irene Antony, Xuyu Qian, Julieta Bonacina, Frances Papandile, Dilenny Gonzalez, Julia Scotellaro, Evan M Bushinsky, Rebecca E Andersen, Eduardo Maury, Len A Pennacchio, Ryan N Doan, Christopher A Walsh
{"title":"Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk.","authors":"Taehwan Shin, Janet H T Song, Michael Kosicki, Connor Kenny, Samantha G Beck, Lily Kelley, Irene Antony, Xuyu Qian, Julieta Bonacina, Frances Papandile, Dilenny Gonzalez, Julia Scotellaro, Evan M Bushinsky, Rebecca E Andersen, Eduardo Maury, Len A Pennacchio, Ryan N Doan, Christopher A Walsh","doi":"10.1016/j.xgen.2024.100609","DOIUrl":"10.1016/j.xgen.2024.100609","url":null,"abstract":"<p><p>Little is known about the role of non-coding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of non-coding regions: human accelerated regions (HARs), which show signatures of positive selection in humans; experimentally validated neural VISTA enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole-genome analysis of >16,600 samples and >4,900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures. We identified multiple patient variants in HARs near IL1RAPL1 and in VEs near OTX1 and SIM1 and showed that they change enhancer activity. Our results implicate both human-evolved and evolutionarily conserved non-coding regions in ASD risk and suggest potential mechanisms of how regulatory changes can modulate social behavior.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100609"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-08-14Epub Date: 2024-07-02DOI: 10.1016/j.xgen.2024.100604
Mireia Ramos-Rodríguez, Marc Subirana-Granés, Richard Norris, Valeria Sordi, Ángel Fernández, Georgina Fuentes-Páez, Beatriz Pérez-González, Clara Berenguer Balaguer, Helena Raurell-Vila, Murad Chowdhury, Raquel Corripio, Stefano Partelli, Núria López-Bigas, Silvia Pellegrini, Eduard Montanya, Montserrat Nacher, Massimo Falconi, Ryan Layer, Meritxell Rovira, Abel González-Pérez, Lorenzo Piemonti, Lorenzo Pasquali
{"title":"Implications of noncoding regulatory functions in the development of insulinomas.","authors":"Mireia Ramos-Rodríguez, Marc Subirana-Granés, Richard Norris, Valeria Sordi, Ángel Fernández, Georgina Fuentes-Páez, Beatriz Pérez-González, Clara Berenguer Balaguer, Helena Raurell-Vila, Murad Chowdhury, Raquel Corripio, Stefano Partelli, Núria López-Bigas, Silvia Pellegrini, Eduard Montanya, Montserrat Nacher, Massimo Falconi, Ryan Layer, Meritxell Rovira, Abel González-Pérez, Lorenzo Piemonti, Lorenzo Pasquali","doi":"10.1016/j.xgen.2024.100604","DOIUrl":"10.1016/j.xgen.2024.100604","url":null,"abstract":"<p><p>Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in β cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of β cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100604"},"PeriodicalIF":11.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11406191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2024-07-10Epub Date: 2024-06-24DOI: 10.1016/j.xgen.2024.100588
Kar-Tong Tan, Michael K Slevin, Mitchell L Leibowitz, Max Garrity-Janger, Jidong Shan, Heng Li, Matthew Meyerson
{"title":"Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing.","authors":"Kar-Tong Tan, Michael K Slevin, Mitchell L Leibowitz, Max Garrity-Janger, Jidong Shan, Heng Li, Matthew Meyerson","doi":"10.1016/j.xgen.2024.100588","DOIUrl":"10.1016/j.xgen.2024.100588","url":null,"abstract":"<p><p>Alterations in the structure and location of telomeres are pivotal in cancer genome evolution. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeats, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. These results provide a framework for the systematic study of telomeric repeats in cancer genomes, which could serve as a model for understanding the somatic evolution of other repetitive genomic elements.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100588"},"PeriodicalIF":11.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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