期刊
NATURE METHODS
卷 18, 期 9, 页码 1046-+出版社
NATURE PORTFOLIO
DOI: 10.1038/s41592-021-01248-7
关键词
-
资金
- National Institutes of Health Common Fund 4D Nucleome Program [U54-DK107980, UM1-HG011536]
- National Human Genome Research Institute (NHGRI) [HG003143]
- Human Frontiers Science Program (HFSP) [LT000631/2017-L]
Chromosome conformation capture assays, such as Hi-C and Micro-C, are used to map chromatin interactions and understand chromosome folding mechanisms. Through systematic evaluation of experimental parameters, an optimized Hi-C protocol was developed for detecting loops and compartments, improving the ability to study chromosome organization.
Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project. This analysis systematically evaluates cross-linking chemistry and chromatin fragmentation strategies commonly used in 3C assays and introduces an improved Hi-C protocol for detecting loops and compartments.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据