Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9

Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number59
JournalGenome biology
Volume21
Issue number1
DOIs
StatePublished - Mar 5 2020

Keywords

  • 3D genome
  • CRISPR/Cas9
  • Chromatin
  • Enhancers
  • Epigenetics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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