Systematic evaluation of chromosome conformation capture assays
| Autor: | René Maehr, Hui Mao, Job Dekker, Johan H. Gibcus, Ryan M.J. Genga, Leonid A. Mirny, Ankita Nand, Oliver J. Rando, Sergey V. Venev, Liyan Yang, Krishna Mohan Parsi, Marlies E. Oomen, Nils Krietenstein, Sameer Abraham, Betul Akgol Oksuz, Hakan Ozadam |
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| Rok vydání: | 2020 |
| Předmět: |
Databases
Factual Computer science Human Embryonic Stem Cells Genomics Computational biology Biology Biochemistry Cell Line Genomic analysis Fragment size Chromosome conformation capture Chromosomes Human Humans Compartment (development) Molecular Biology Protocol (science) Chromosome Cell Biology Chromatin Folding (chemistry) Cross-Linking Reagents Genetic Techniques Preprint Analysis Biotechnology |
| Zdroj: | Nature Methods |
| DOI: | 10.1101/2020.12.26.424448 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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