2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing
Abstract Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughpu...
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doaj-c42efafcb2e14cee9062b99d184e3af92020-11-25T01:02:20ZengBMCBMC Genomics1471-21642019-02-0120111610.1186/s12864-019-5532-52C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencingXue Qing David Wang0Christopher J. F. Cameron1Denis Paquette2Dana Segal3Reid Warsaba4Mathieu Blanchette5Josée Dostie6Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversityDepartment of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversityDepartment of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversityDepartment of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversityDepartment of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversitySchool of Computer Science and McGill Center for Bioinformatics, McGill UniversityDepartment of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill UniversityAbstract Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. Results Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. Conclusions 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis.http://link.springer.com/article/10.1186/s12864-019-5532-5Chromatin immunoprecipitationNext-generation sequencingLigation-mediated amplificationEpigeneticsHOXDifferentiation |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xue Qing David Wang Christopher J. F. Cameron Denis Paquette Dana Segal Reid Warsaba Mathieu Blanchette Josée Dostie |
spellingShingle |
Xue Qing David Wang Christopher J. F. Cameron Denis Paquette Dana Segal Reid Warsaba Mathieu Blanchette Josée Dostie 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing BMC Genomics Chromatin immunoprecipitation Next-generation sequencing Ligation-mediated amplification Epigenetics HOX Differentiation |
author_facet |
Xue Qing David Wang Christopher J. F. Cameron Denis Paquette Dana Segal Reid Warsaba Mathieu Blanchette Josée Dostie |
author_sort |
Xue Qing David Wang |
title |
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
title_short |
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
title_full |
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
title_fullStr |
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
title_full_unstemmed |
2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
title_sort |
2c-chip: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-02-01 |
description |
Abstract Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. Results Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. Conclusions 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis. |
topic |
Chromatin immunoprecipitation Next-generation sequencing Ligation-mediated amplification Epigenetics HOX Differentiation |
url |
http://link.springer.com/article/10.1186/s12864-019-5532-5 |
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