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

doi:10.1186/s13059-020-01973-w

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

Genome Biol. 2020 Mar 5;21(1):59. doi: 10.1186/s13059-020-01973-w.

Authors

Xin Liu^{1

2}, Yong Chen^{3

4}, Yuannyu Zhang^{1

2}, Yuxuan Liu^{1

2}, Nan Liu⁵, Giovanni A Botten^{1

2}, Hui Cao^{1

2}, Stuart H Orkin^{5

6}, Michael Q Zhang³, Jian Xu^{7

8}

Affiliations

¹ Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
² Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
³ Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA.
⁴ Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ, 08028, USA.
⁵ Division of Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute and Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.
⁶ Howard Hughes Medical Institute, Boston, MA, 02115, USA.
⁷ Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. jian.xu@utsouthwestern.edu.
⁸ Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. jian.xu@utsouthwestern.edu.

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.

Keywords: 3D genome; CRISPR/Cas9; Chromatin; Enhancers; Epigenetics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Biotinylation
CRISPR-Associated Protein 9*
Cell Differentiation / genetics
Chromatin / chemistry*
Enhancer Elements, Genetic*
Erythroid Cells
Genetic Loci
Locus Control Region
Promoter Regions, Genetic*
beta-Globins / genetics

Substances

Chromatin
beta-Globins
CRISPR-Associated Protein 9

Abstract

Publication types

MeSH terms

Substances

Grants and funding