The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.
Liu, Xin; Chen, Yong; Zhang, Yuannyu; Liu, Yuxuan; Liu, Nan; Botten, Giovanni A; Cao, Hui; Orkin, Stuart H; Zhang, Michael Q; and Xu, Jian, "Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9." (2020). Faculty Scholarship for the College of Science & Mathematics. 166.
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Liu, X., Chen, Y., Zhang, Y. et al. (2020). Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol 21, 59 (2020). https://doi.org/10.1186/s13059-020-01973-w