Chromatin-Associated RNA Sequencing (ChAR-seq).

Autor: Jukam D; Department of Biology, Stanford University, Stanford, California., Limouse C; Department of Biochemistry, Stanford University School of Medicine, Stanford, California., Smith OK; Department of Biochemistry, Stanford University School of Medicine, Stanford, California.; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California., Risca VI; Department of Genetics, Stanford University School of Medicine, Stanford, California.; Present Address: Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, New York., Bell JC; Department of Biochemistry, Stanford University School of Medicine, Stanford, California.; Present Address: 10X Genomics, Pleasanton, California., Straight AF; Department of Biochemistry, Stanford University School of Medicine, Stanford, California.; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California.
Jazyk: angličtina
Zdroj: Current protocols in molecular biology [Curr Protoc Mol Biol] 2019 Apr; Vol. 126 (1), pp. e87. Date of Electronic Publication: 2019 Feb 20.
DOI: 10.1002/cpmb.87
Abstrakt: RNA is a fundamental component of chromatin. Noncoding RNAs (ncRNAs) can associate with chromatin to influence gene expression and chromatin state; many also act at long distances from their transcriptional origin. Yet we know almost nothing about the functions or sites of action for most ncRNAs. Current methods to identify sites of RNA interaction with the genome are limited to the study of a single RNA at a time. Here we describe a protocol for ChAR-seq, a strategy to identify all chromatin-associated RNAs and map their DNA contacts genome-wide. In ChAR-seq, proximity ligation of RNA and DNA to a linker molecule is used to construct a chimeric RNA-DNA molecule that is converted to DNA for sequencing. In a single assay, ChAR-seq can discover de novo chromatin interactions of distinct RNAs, including nascent transcripts, splicing RNAs, and long noncoding RNAs (lncRNAs). Resulting "maps" of genome-bound RNAs should provide new insights into RNA biology. © 2019 by John Wiley & Sons, Inc.
(© 2019 John Wiley & Sons, Inc.)
Databáze: MEDLINE
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