2C-ChIP maps of chromatin state at the HOXA gene locus in NT2-D1 cells

Understanding how transcription occurs will require integrating genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in genomics studies, and while genome-wide methods are available, there is a lack in high-throughput approaches to analyze defined regions. Here, we present ‘2C-ChIP’, a versatile, inexpensive, and high-throughput method to quantitatively measure the abundance of DNA sequences in ChIP samples. 2C-ChIP recapitulates results from benchmark approaches used as ChIP readout. We applied 2C-ChIP to the HOXA cluster and find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA enhancing gene expression during differentiation.