Identification of RNF2-responding loci in long-range chromatin interactions using the novel 4C-ChIP-Cloning technology.

RNF2 is a core component of Polycomb repressive complex 1 (PRC1), which binds to various chromatic regions to regulate their transcriptional activity. It was recently reported that EZH2, a Polycomb group complex member, helps mediate long-range chromosomal interactions in mammalian cells. The present study investigates whether RNF2-responding loci interact in long-range chromatin. The new 4C-ChIP-Cloning technology was developed based on circular chromosome conformation capture (4C) and ChIP. Use of the 4C-ChIP-Cloning technology successfully identified four loci in long-range cis- or trans-interactions that were mediated by the RNF2 protein. RNAi experiments showed that RNF2 regulated the transcription levels of genes adjacent to the loci. These results suggest that RNF2 protein, as part of PRC1, mediates long-range interactions between RNF2-interation loci and regulates adjacent genes. This 4C-ChIP-Cloning technology may contribute to the study of protein-mediated long-range chromatin interactions with specific regulatory elements.