Open AccessDetermination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system
Author(s) -
Qiu Wan-hua,
Zhijiao Xu,
Min Zhang,
Dandan Zhang,
Hui Fan,
Taotao Li,
Qianfeng Wang,
Peiru Liu,
Zaihua Zhu,
Duo Du,
Minjia Tan,
Bo Wen,
Yun Liu
Publication year - 2019
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkz134
Subject(s) - biology , chromatin , crispr , locus (genetics) , genetics , telomere , computational biology , genome , rna , dna , gene
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.