Whole genome chromatin interaction analysis using paired end diTags

AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore A51 The human genome is organized into high level structures, and DNA elements separated by long genomic distances could functionally interact. We developed a method for whole genome chromatin interaction analysis using paired end ditag sequencing (ChIA-PET) to reveal long-range interactions mediated by transcription factors. In this method, chromatin is cross-linked and sonicated; the resulting protein/DNA complexes are ligated to a specific linker containing two type IIs restriction enzyme recognition sites, and digested to release paired end ditags (PETs) for high throughput sequencing. The sequences are mapped to the reference genome and clustered to identify transcription factor binding sites (TFBS) as well as long-range interactions between the TFBS. We validated this approach by mapping whole genome chromatin interactions mediated by estrogen receptor α (ERα) in human breast cancer cells. We identified 472 high-confidence and 1,910 medium-confidence intrachromosomal long-range interactions between ERα binding sites. Many long-range interactions involve multiple ERα binding sites, suggesting complex regulation by ERα. ChIP-3C was successfully used to validate 15 interactions present near 10 genes. Our results demonstrate that ChIA-PET is an unbiased approach for whole genome high-throughput analysis of long-range chromatin interactions, and that intrachromosomal long-range interactions between TFBS constitute a primary mechanism for ERα-mediated function.