Systematic evaluation of chromosome conformation capture assays
Nat Methods. 2021-09-03;18(9):1046-1055.
- Abstract
- 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.
- Datasets
- DSR537RIC, DSR444FBP, DSR807ISC, DSR155TYW, DSR422CEP, DSR327HLB, DSR091MER, DSR180QGS, DSR055LFO, DSR737KGH, DSR391QNO, DSR700PCF, DSR684ZGS, DSR918CIC, DSR047QKB, DSR479GVD, DSR872POY, DSR048TYT, DSR653MUU, DSR066YTQ, DSR754YHM, DSR149PDL, DSR490EZC, DSR767WND, DSR572IKT, DSR254PGW, DSR289YIM, DSR451EJU, DSR157LBO, DSR896FIE, DSR811XDN, DSR671AAD, DSR549RIC, DSR124JOP, DSR507LIX, DSR586PLM, DSR731TDZ, DSR316HBX, DSR540FLU, DSR456FWD, DSR090OCI, DSR564AJF, DSR533TGW, DSR397ZND, DSR106XXT, DSR169IMD, DSR012WQO, DSR483MTK, DSR312WNM, DSR841NPK, DSR045HCZ, DSR748OFL, DSR969OFL, DSR891WEA, DSR567IUM, DSR497DAF, DSR119YGF, DSR499WVQ, DSR072SNV, DSR000VQE, DSR951IQG, DSR495LNB, DSR324ANW, DSR457HRL, DSR884KPT, DSR313XKJ, DSR378EON, DSR882XCP, DSR407FUO, DSR851OCU, DSR919SOB, DSR558JJA, DSR075HLG, DSR231TYR, DSR961WJW, DSR834ANZ, DSR223YPR, DSR636IVC, DSR311UIT, DSR852XHU, DSR721YOW, DSR437FIX, DSR287QTC, DSR037DPN, DSR832OKT, DSR654AVA, DSR949CFE, DSR049XUF, DSR181EFP, DSR010WGH, DSR725VAR, DSR139UBN, DSR310VWE, DSR613OLV, DSR915YYD, DSR737EQA, DSR538ETS, DSR290BVC, DSR440NHM, DSR544NFB, DSR665NMH, DSR845GYW, DSR680GUA, DSR229MMI, DSR459WFJ, DSR586GXI, DSR527MQI, DSR513QXR, DSR025KNY, DSR976HAN, DSR575SAL, DSR151HTH, DSR247WWZ, DSR718IEG, DSR366YRD, DSR710ZMS, DSR358YIW, DSR242UWU, DSR272NBQ, DSR998VIS, DSR345JDI, DSR585LXT, DSR792YFU, DSR111BUL, DSR056YFO, DSR638LLT, DSR707LEZ, DSR531OKL, DSR105EMA
Related data
- Data summary
- Data are available at GEO under accession number GSE163666. Supplementary Table 1 lists datasets accessible through the 4DN data portal including 4DN accession numbers. Source data are provided with this paper.
- Available data
- website
- Data summary
- Scripts and notebooks used in this paper can be accessed at https://github.com/dekkerlab/matrix_paper