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Nat Methods. 2019 Jun;16(6):489-492. doi: 10.1038/s41592-019-0407-x. Epub 2019 May 27.

HiChIRP reveals RNA-associated chromosome conformation.

Author information

1
Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
2
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
3
Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA.
4
Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
5
Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
6
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
7
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
8
Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA.
9
Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
10
Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. wjg@stanford.edu.
11
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. wjg@stanford.edu.
12
Department of Applied Physics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
13
Chan Zuckerberg Biohub, San Francisco, CA, USA. wjg@stanford.edu.
14
Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
15
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
16
Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
17
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.

Abstract

Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).

PMID:
31133759
PMCID:
PMC6638558
DOI:
10.1038/s41592-019-0407-x
[Indexed for MEDLINE]
Free PMC Article

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