Theme

Long-range gene regulatory interactions are defined as interactions between a region of regulatory DNA sequence and a target gene that can be hundreds of kilobases away. Such interactions are emerging as important determinants of cell type specific expression, and, the effect of regulatory sequence variants on complex phenotypes including those associated with diseases. The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the availability of chromosome conformation capture (3C) data sets that characterize the 3D organization of chromatin at a genome-wide scale. This organization, also referred to as the 3D nucleome, is not only important for packing the genome into the nucleus but also has significant impact on how the genome functions. With the emergence of these new data types there is an increasingly growing demand for computational tools that can systematically analyze these data. These tools range from data processing issues (e.g. mapping and normalization) to data analysis issues such as prediction of chromosomal organizational units (e.g. TADs), identifying significant interactions between regulatory elements (e.g. enhancer-promoter), examining the interplay of transcription factors, architectural proteins and chromatin states in establishing these interactions, and, examining how these interactions are impacted by sequence variants.

In the past year, NIH has funded several 4D nucleome centers for studies of the 3D nucleome with one additional dimension, such as developmental time, disease progression, with the aim of linking distal regulatory elements identified by GWAS, ENCODE or other studies to their target genes. In just the past few months the field has seen several novel technologies related to profiling 3D nucleome using imaging, single cell techniques and ChIP-based enrichment. Therefore, we believe this is a very timely session and that it will promote involvement of more bioinformatics researchers (junior and senior scientists) in this young and exciting field of genome organization in gene regulation. In this session, we plan to have invited and contributed talks from prominent scientists who are at the forefront of developing new tools and techniques in the field.

Session Plan

This session will be interesting for researchers at all levels (undergraduate, graduate, postdoctoral, faculty, next-generation sequencing-related industry) working in the broad fields of computational systems biology, transcriptional gene regulation and gene regulatory networks, and genetic variation. We have invited two senior researchers who we wish to designate as keynotes. In addition, we have two more speakers who are doing cutting edge work in the field of chromatin biology and 3D gene regulation.