Paired-End Tags For Unravelling Genomic Elements And Chromantin Interactions

Abstract

Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. In particular, one of the most important questions in gene expression regulation is how remote control of transcription regulation in a complex genome is organized. The Paired-End Tag (PET) strategy involves extraction of paired short tags from the ends of linear DNA fragments for ultra-high-throughput sequencing. In addition to new methods of constructing PETs, here I show a novel application of PET in understanding molecular interactions between distant genomic elements. Using this Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing method, I present the first-ever global estrogen receptor N1-mediated human interactome chromatin map. I show that chromatin interactions are important in gene regulation. With its versatile and powerful nature, the PET sequencing strategies and the new application, ChIA-PET, have a bright future ahead.