UNIVERSITY OF MASSACHUSETTS
This award is part of the ENCODE consortium and aims to 1) identify novel long-range acting gene regulatory elements and 2) to link these elements to specific (distant) target genes. This grant focuses on 1% of the human genome that was selected by the ENCODE pilot project and employs 5C technology to comprehensively map long-range looping interactions between promoters and distal functional elements. The purpose of this supplement is to 1) significantly increase the breadth of our analysis by identifying more classes of long-range acting functional elements; and 2) to increase the depth of our understanding of 5C data by developing novel computational approaches for data analysis. We propose to increase the breadth of our analysis by generating new types of 5C long-range interaction maps. The parent grant focuses on long-range interactions that involve promoters. In order to obtain a more comprehensive set of long-range acting functional elements we propose to generate two new 5C maps: we propose to generate 5C maps that interrogate all long-range interactions that involve insulators and 5C maps that interrogate all looping interactions that involve enhancers. These maps will be generated for the 44 ENCODE regions in the same cell lines that were used for generating the 5C promoter maps (GM12878 and K562). To generate these maps we will use enhancer and insulator elements that have been identified in K562 and GM12878 cells by the ENCODE consortium. We propose to increase the depth of our understanding of 5C data by developing novel analysis methodologies that mine the rich 5C dataset at multiple levels: 1) we aim to identify specific functional elements that loop to specific other elements. 2) We will develop methods to identify larger chromosomal domains and characterize the functional elements that define their boundaries. 3) We will explore network-based approaches to better characterize the complex topology of long-range chromatin interaction networks.