2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing

BMC Genomics
Xue Qing David WangJosée Dostie

Abstract

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.

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Citations

Jun 5, 2020·BMC Research Notes·Christopher J F CameronMathieu Blanchette

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Datasets Mentioned

BETA
SRP155022

Methods Mentioned

BETA
immunoprecipitation
ChIP
ChIP-seq
PCRs
ChIPs
immunoprecipitations
PCR
transfection
pull down
Assay

Software Mentioned

Oligo Calc
BLAST
OligoCalc
- heatmap
my5C

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