Recent studies have provided substantial evidence that the genome consists not merely of linear structures but rather it is folded into elaborate patterns that permits interactions between genomic elements separated by large genomic distances. The precise folding and the spectrum of topologies of the genome remain to be determined. Recent studies have provided insight into the 3D-architectures of the immunoglobulin heavy chain (Igh) and ?-globin loci. These data have revealed that these loci are organized into multiple compartments that are characterized by bundles of loops, consistent with the Multiple-Loop-Subcompartment (MLS) Model. We are now faced with the question as to whether the entire genome is folded as proposed by the MLS model. To address this question, we have recently employed a formaldehyde cross-linking approach that permits the identification of a genome-wide network of interacting genomic elements in pro-B cells. Our preliminary data indicates that the pro-B cell genome indeed is organized into clusters of loops that are connected by linkers as predicted by the MLS model. Here we would propose to continue these studies. We would perform an in depth analysis of individual compartments and examine how they are organized and how they relate to B-lineage specific programs of gene expression. We would identify and characterize intra-chromosomal interactions. Insulators and bridging factors would be identified and characterized both from a biochemical and functional perspective. Finally, we propose to determine the structure of mitotic chromosomes in pre-pro-B and pro-B cells. The overall goal would be to decipher the spectrum of conformations and trajectories formed by the pre-pro-B and pro-B cell chromatin fibers and how chromatin structure relates to function.

Public Health Relevance

The proposal described here is aimed at developing a novel approach to describe the folding of the chromatin fiber in pre-pro-B and pro-B cells. The study would provide physical insight into the mechanism that permits enhancer and promoter elements to interact with each other with the appropriate frequencies in order to modulate down- stream target gene expression. The studies may also provide insight into the mechanisms that underpin genomic instability.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01AI100880-03
Application #
8653532
Study Section
Cellular and Molecular Immunology - A Study Section (CMIA)
Program Officer
Nasseri, M Faraz
Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Diego
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Miyazaki, Kazuko; Miyazaki, Masaki; Murre, Cornelis (2014) The establishment of B versus T cell identity. Trends Immunol 35:205-10
Lucas, Joseph S; Zhang, Yaojun; Dudko, Olga K et al. (2014) 3D trajectories adopted by coding and regulatory DNA elements: first-passage times for genomic interactions. Cell 158:339-52
Lin, Yin C; Murre, Cornelis (2013) Nuclear location and the control of developmental progression. Curr Opin Genet Dev 23:104-8