2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.
5C
Chromatin immunoprecipitation
Differentiation
Epigenetics
HOX
Ligation-mediated amplification
Long non-coding RNA
Next-generation sequencing
Transcription
subTAD
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
28 Feb 2019
28 Feb 2019
Historique:
received:
06
08
2018
accepted:
15
02
2019
entrez:
2
3
2019
pubmed:
2
3
2019
medline:
14
6
2019
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
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
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.
Identifiants
pubmed: 30819105
doi: 10.1186/s12864-019-5532-5
pii: 10.1186/s12864-019-5532-5
pmc: PMC6394006
doi:
Substances chimiques
RNA, Long Noncoding
0
long noncoding RNA HOXA-AS2, human
0
Types de publication
Journal Article
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
162Subventions
Organisme : Canadian Institutes of Health Research
ID : 142451
Pays : Canada
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