通过 ViCAR 改进表观遗传特征和三维染色质结构的同步绘图

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-09-03 DOI:10.1186/s13059-024-03377-6

Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian

{"title":"通过 ViCAR 改进表观遗传特征和三维染色质结构的同步绘图","authors":"Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian","doi":"10.1186/s13059-024-03377-6","DOIUrl":null,"url":null,"abstract":"Methods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). To bridge this gap, we introduce ViCAR (viewpoint HiCAR), for the direct antibody-based capture of chromatin interactions at folded G4s. Through ViCAR, we showcase the first G4-3D interaction landscape. Using histone marks, we also demonstrate how ViCAR improves on earlier approaches yielding increased signal-to-noise. ViCAR is a practical and powerful tool to explore epigenetic marks and 3D genome interactomes.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"9 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR\",\"authors\":\"Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian\",\"doi\":\"10.1186/s13059-024-03377-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Methods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). To bridge this gap, we introduce ViCAR (viewpoint HiCAR), for the direct antibody-based capture of chromatin interactions at folded G4s. Through ViCAR, we showcase the first G4-3D interaction landscape. Using histone marks, we also demonstrate how ViCAR improves on earlier approaches yielding increased signal-to-noise. ViCAR is a practical and powerful tool to explore epigenetic marks and 3D genome interactomes.\",\"PeriodicalId\":12611,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"9 1\",\"pages\":\"\"},\"PeriodicalIF\":10.1000,\"publicationDate\":\"2024-09-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-024-03377-6\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-024-03377-6","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

测量组蛋白修饰或蛋白质结合的基因组区域染色质接触的方法是研究染色质组织的重要工具。然而，这些方法并不能捕捉到其他表观基因组特征的可能参与，如 G-四叠体 DNA 二级结构（G4s）。为了弥补这一缺陷，我们推出了 ViCAR（观点 HiCAR），用于基于抗体直接捕获折叠 G4s 上的染色质相互作用。通过 ViCAR，我们首次展示了 G4-3D 相互作用图谱。通过组蛋白标记，我们还展示了 ViCAR 如何改进早期方法，提高信噪比。ViCAR 是探索表观遗传标记和三维基因组相互作用组的实用而强大的工具。

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

Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR

Methods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). To bridge this gap, we introduce ViCAR (viewpoint HiCAR), for the direct antibody-based capture of chromatin interactions at folded G4s. Through ViCAR, we showcase the first G4-3D interaction landscape. Using histone marks, we also demonstrate how ViCAR improves on earlier approaches yielding increased signal-to-noise. ViCAR is a practical and powerful tool to explore epigenetic marks and 3D genome interactomes.

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

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.