1. 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.
- Author
-
Wang XQD, Cameron CJF, Paquette D, Segal D, Warsaba R, Blanchette M, and Dostie J
- Subjects
- Cell Differentiation genetics, Cells, Cultured, Epigenesis, Genetic, Gene Expression, Genes, Homeobox, Genomics, Humans, RNA, Long Noncoding physiology, Real-Time Polymerase Chain Reaction, Chromatin Immunoprecipitation methods, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA
- 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.
- Published
- 2019
- Full Text
- View/download PDF