Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology; Program in Molecular Medicine; Diabetes Center of Excellence; Graduate School of Biomedical Sciences
Biochemistry, Biophysics, and Structural Biology | Genetics and Genomics
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.
Genomic analysis, Genomics
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DOI of Published Version
Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Systematic evaluation of chromosome conformation capture assays. Nat Methods. 2021 Sep;18(9):1046-1055. doi: 10.1038/s41592-021-01248-7. Epub 2021 Sep 3. PMID: 34480151; PMCID: PMC8446342. Link to article on publisher's site
Akgol-Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga R, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. (2021). Systematic evaluation of chromosome conformation capture assays. Program in Molecular Medicine Publications. https://doi.org/10.1038/s41592-021-01248-7. Retrieved from https://escholarship.umassmed.edu/pmm_pp/149
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This work is licensed under a Creative Commons Attribution 4.0 License.