新兴的三维基因组组织序列语法。

IF 3.6 2区生物学 Q2 GENETICS & HEREDITY

Human Genetics Pub Date : 2025-10-01 Epub Date: 2025-08-25 DOI:10.1007/s00439-025-02772-8

Liezel Tamon, James Ashford, Matthew Nicholls, Marella F T R de Bruijn, Aleksandr B Sahakyan

{"title":"新兴的三维基因组组织序列语法。","authors":"Liezel Tamon, James Ashford, Matthew Nicholls, Marella F T R de Bruijn, Aleksandr B Sahakyan","doi":"10.1007/s00439-025-02772-8","DOIUrl":null,"url":null,"abstract":"The multiplexed layers of regulatory processes and mechanisms within a cell are, to a degree, encoded in our genome. Unravelling the relationship between DNA sequence and molecular processes is crucial for understanding evolution, interpreting and predicting the consequences of genomic variation. Furthermore, understanding the extent to which DNA sequence contributes to the genome organisation can help reveal the aspects more influenced by other factors. Therefore, here we provide a succinct summary of the emerging genomic sequence code or \"grammar\" of genomic contact formation and 3D genome organisation. Drawing on different types of evidence from multiple disciplines, from large-scale genomic studies, biochemical in vitro assays, and computational analyses utilising machine learning and other modelling techniques, we aim to inform future research on the present associations between 3D genome organisation and sequence.","PeriodicalId":13175,"journal":{"name":"Human Genetics","volume":" ","pages":"917-928"},"PeriodicalIF":3.6000,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12476417/pdf/","citationCount":"0","resultStr":"{\"title\":\"The emerging sequence grammar of 3D genome organisation.\",\"authors\":\"Liezel Tamon, James Ashford, Matthew Nicholls, Marella F T R de Bruijn, Aleksandr B Sahakyan\",\"doi\":\"10.1007/s00439-025-02772-8\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The multiplexed layers of regulatory processes and mechanisms within a cell are, to a degree, encoded in our genome. Unravelling the relationship between DNA sequence and molecular processes is crucial for understanding evolution, interpreting and predicting the consequences of genomic variation. Furthermore, understanding the extent to which DNA sequence contributes to the genome organisation can help reveal the aspects more influenced by other factors. Therefore, here we provide a succinct summary of the emerging genomic sequence code or \\\"grammar\\\" of genomic contact formation and 3D genome organisation. Drawing on different types of evidence from multiple disciplines, from large-scale genomic studies, biochemical in vitro assays, and computational analyses utilising machine learning and other modelling techniques, we aim to inform future research on the present associations between 3D genome organisation and sequence.\",\"PeriodicalId\":13175,\"journal\":{\"name\":\"Human Genetics\",\"volume\":\" \",\"pages\":\"917-928\"},\"PeriodicalIF\":3.6000,\"publicationDate\":\"2025-10-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12476417/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Human Genetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1007/s00439-025-02772-8\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/8/25 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Human Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s00439-025-02772-8","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/8/25 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

摘要

细胞内的多层调控过程和机制在某种程度上是由我们的基因组编码的。揭示DNA序列和分子过程之间的关系对于理解进化、解释和预测基因组变异的后果至关重要。此外，了解DNA序列对基因组组织的贡献程度可以帮助揭示受其他因素影响更大的方面。因此，在这里，我们提供了一个新兴的基因组序列代码或基因组接触形成和三维基因组组织的“语法”的简洁总结。利用来自多个学科的不同类型的证据，从大规模基因组研究，体外生化分析，以及利用机器学习和其他建模技术的计算分析，我们的目标是为3D基因组组织和序列之间的当前关联的未来研究提供信息。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

The emerging sequence grammar of 3D genome organisation.

The multiplexed layers of regulatory processes and mechanisms within a cell are, to a degree, encoded in our genome. Unravelling the relationship between DNA sequence and molecular processes is crucial for understanding evolution, interpreting and predicting the consequences of genomic variation. Furthermore, understanding the extent to which DNA sequence contributes to the genome organisation can help reveal the aspects more influenced by other factors. Therefore, here we provide a succinct summary of the emerging genomic sequence code or "grammar" of genomic contact formation and 3D genome organisation. Drawing on different types of evidence from multiple disciplines, from large-scale genomic studies, biochemical in vitro assays, and computational analyses utilising machine learning and other modelling techniques, we aim to inform future research on the present associations between 3D genome organisation and sequence.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Human Genetics 生物-遗传学

CiteScore

10.80

自引率

3.80%

发文量

审稿时长

1 months

期刊介绍： Human Genetics is a monthly journal publishing original and timely articles on all aspects of human genetics. The Journal particularly welcomes articles in the areas of Behavioral genetics, Bioinformatics, Cancer genetics and genomics, Cytogenetics, Developmental genetics, Disease association studies, Dysmorphology, ELSI (ethical, legal and social issues), Evolutionary genetics, Gene expression, Gene structure and organization, Genetics of complex diseases and epistatic interactions, Genetic epidemiology, Genome biology, Genome structure and organization, Genotype-phenotype relationships, Human Genomics, Immunogenetics and genomics, Linkage analysis and genetic mapping, Methods in Statistical Genetics, Molecular diagnostics, Mutation detection and analysis, Neurogenetics, Physical mapping and Population Genetics. Articles reporting animal models relevant to human biology or disease are also welcome. Preference will be given to those articles which address clinically relevant questions or which provide new insights into human biology. Unless reporting entirely novel and unusual aspects of a topic, clinical case reports, cytogenetic case reports, papers on descriptive population genetics, articles dealing with the frequency of polymorphisms or additional mutations within genes in which numerous lesions have already been described, and papers that report meta-analyses of previously published datasets will normally not be accepted. The Journal typically will not consider for publication manuscripts that report merely the isolation, map position, structure, and tissue expression profile of a gene of unknown function unless the gene is of particular interest or is a candidate gene involved in a human trait or disorder.