Determination of Local Chromatin Interactions Using a Combined CRISPR and Peroxidase APEX2 System

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Feb 27

PMID 30805613

Citations 25

Authors

Wenqing Qiu

Zhijiao Xu

Min Zhang

Dandan Zhang

Hui Fan

Taotao Li

Qianfeng Wang

Peiru Liu

Zaihua Zhu

Duo Du

Minjia Tan

Bo Wen

Yun Liu

Affiliations

Soon will be listed here.

Abstract

The architecture and function of chromatin are largely regulated by local interacting molecules, such as transcription factors and noncoding RNAs. However, our understanding of these regulatory molecules at a given locus is limited because of technical difficulties. Here, we describe the use of Clustered Regularly Interspaced Short Palindromic Repeats and an engineered ascorbate peroxidase 2 (APEX2) system to investigate local chromatin interactions (CAPLOCUS). We showed that with specific small-guide RNA targets, CAPLOCUS could efficiently identify both repetitive genomic regions and single-copy genomic locus with high resolution. Genome-wide sequencing revealed known and potential long-range chromatin interactions for a specific single-copy locus. CAPLOCUS also identified telomere-associated RNAs. CAPLOCUS, followed by mass spectrometry, identified both known and novel telomere-associated proteins in their native states. Thus, CAPLOCUS may be a useful approach for studying local interacting molecules at any given chromosomal location.

Citing Articles

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