Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system

Nucleic Acids Research
Wenqing QiuYun Liu

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.

References

Jan 15, 2000·Science·J W Shay, W E Wright
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Oct 16, 2002·Nature Genetics·Marta García-CaoMaría A Blasco
Jul 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Yuko MochizukiPhilip J Mason
Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Oct 3, 2008·Genome Biology·Huawei XinZhou Songyang
Jan 13, 2009·Cell·Jérôme Déjardin, Robert E Kingston
Apr 10, 2009·Annual Review of Biochemistry·Cedric R Clapier, Bradley R Cairns
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Aug 25, 2009·Nature·Yoshiko MaidaKenkichi Masutomi
Nov 6, 2009·Nature·Melissa J FullwoodYijun Ruan
Mar 20, 2010·Cold Spring Harbor Perspectives in Biology·Thomas Cremer, Marion Cremer
May 13, 2010·Nucleic Acids Research·Sophie RedonJoachim Lingner
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Feb 24, 2011·Current Opinion in Genetics & Development·Guohong Li, Danny Reinberg
Apr 2, 2011·The Journal of Biological Chemistry·Richard ChienKyoko Yokomori
Dec 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Matthew D SimonRobert E Kingston
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Jul 19, 2013·Nature Communications·Feng ZhouJarrod A Marto
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Sep 14, 2013·Nucleic Acids Research·Stephanie D ByrumAlan J Tackett
Nov 10, 2013·Science·Natalia NaumovaJob Dekker
Apr 23, 2014·Nature Biotechnology·Xuebing WuPhillip A Sharp
Aug 26, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Zachary J WaldripAlan J Tackett
Nov 2, 2014·Nature Communications·Antonio PorroJoachim Lingner

❮ Previous
Next ❯

Citations

Jun 3, 2020·Cold Spring Harbor Symposia on Quantitative Biology·Furqan M Fazal, Howard Y Chang
Sep 11, 2020·Wiley Interdisciplinary Reviews. Developmental Biology·Justin A BoschNorbert Perrimon
Jun 2, 2020·Frontiers in Genetics·Henning Ummethum, Stephan Hamperl
Jun 26, 2020·Molecular Biotechnology·Zhixi LiuHongtao Xiao
Aug 28, 2020·Frontiers in Cell and Developmental Biology·William A Scott, Eric I Campos
Jun 10, 2020·In Vitro Cellular & Developmental Biology. Animal·Atsushi KuniiTetsushi Sakuma
Mar 11, 2020·Nature Methods·Mathilde GauchierJérôme Déjardin
Nov 14, 2019·Biochemistry·Thanh My Thi NguyenMihye Lee
Jan 13, 2021·Nature Methods·Wei QinAlice Y Ting
Apr 27, 2021·Plant Communications·Xinxin YangYongliang Zhang
Jul 14, 2020·Journal of the American Chemical Society·Jerrin Thomas GeorgeSeergazhi G Srivatsan
Sep 24, 2021·Genomics, Proteomics & Bioinformatics·Xinran LiHaiyun Gan
Oct 29, 2021·Biochemical Society Transactions·Antony J BurtonTom W Muir
Oct 19, 2021·Plant Physiology·Andrea Mair, Dominique C Bergmann

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE114133

Methods Mentioned

BETA
immunoprecipitation
ChIP
PCR
RNA-Seq
pull-down
electrophoresis
pull down
acetylation
affinity purification
ChIP-Seq

Software Mentioned

picard
4C
pxMARGI
IGV
GenomicRanges
Circos
BioID
MaxQuant
bedtools
R package clusterProfiler

Related Concepts

Related Feeds

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

CRISPR Genome Editing & Therapy

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on the application of this system for gene editing and therapy in human diseases.

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.