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

Genome Biology
Xin LiuJian Xu

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.

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Citations

Mar 21, 2021·Current Opinion in Hematology·Marlies P Rossmann, Leonard I Zon
Nov 22, 2020·Current Opinion in Genetics & Development·Sjoerd Jd Tjalsma, Wouter de Laat
Jun 19, 2021·Molecular Biology Reports·Kirti PrasadKumarasamypet M Mohankumar
Aug 19, 2021·Nature Communications·Yong ShenVijay G Sankaran
Oct 29, 2021·Biochemical Society Transactions·Antony J BurtonTom W Muir

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Datasets Mentioned

BETA
GSM2400133
GSM970213
GSM970216
GSM2037371
GSM27050435
GSM1370434
GSM1370436
GSM1551618

Methods Mentioned

BETA
proximity ligation
Hi-C
Affinity Purification
ChIP
RNA-seq
transgenic
dissection
ChIP-seq
BioSample
PCR

Software Mentioned

Bowtie2
Cufflinks
GENCODE
MACS
CAPTURE1
RSEM
CAPTURE2
deepTools2
HOMER
GraphPad Prism

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