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

• Main Authors: Xue Qing David Wang, Christopher J. F. Cameron, Denis Paquette, Dana Segal, Reid Warsaba, Mathieu Blanchette, Josée Dostie
• Format: Article
• Language: English
• Published: BMC 2019-02-01
• Series: BMC Genomics
• Subjects: Chromatin immunoprecipitation; Next-generation sequencing; Ligation-mediated amplification; Epigenetics; HOX; Differentiation
• Online Access: http://link.springer.com/article/10.1186/s12864-019-5532-5

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.