The long-range goals of the research proposed in this application are to determine at high resolution the 3D-structure of the immunoglobulin heavy chain (Igh) locus. The Igh locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. To probe the topography of the Igh locus, we have recently determined the spatial distance distributions using 12 genomic markers that spanned the entire locus. These spatial distance distributions were compared to computer simulations of alternative chromatin arrangements. This analysis predicted that the Igh locus is organized into compartments containing clusters of loops separated by linkers. We then used computational geometry to determine the mean relative 3D-positions of the VH, DH, JH and CH elements. Briefly, the data showed that during early B cell development, the entire repertoire of VH regions (2.5 Mbp) is merged and juxtaposed to the DH elements, allowing the VH regions to encounter DHJH elements with relatively high and similar frequencies. Here we propose to continue these studies. We would describe at high resolution the average Igh locus trajectories in interphase and mitotic chromatin. We would determine the spectrum of conformations adopted by the Igh locus fiber. We would use structured illumination microscopy to visualize the Igh chromatin territories. We would characterize compartments using physical approaches. We would identify loop bases using both physical and molecular biological approaches. We would use spatial distance measurements and computational geometry to determine whether the Igh locus structure is a general feature of antigen receptor loci and eukaryotic interphase chromatin. Taken together, these studies would provide a statistical description of Igh locus structure and provide mechanistic insight into how antibody diversity is generated.

Public Health Relevance

In previous studies we have used geometry to show how a genetic locus is organized in 3D space. The studies proposed in this application should provide insight into how the structure of the genome permits the generation of an immune response to a wide variety of invading pathogens.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI082850-04
Application #
8223186
Study Section
Special Emphasis Panel (ZRG1-IMM-H (02))
Program Officer
Nasseri, M Faraz
Project Start
2009-03-01
Project End
2014-02-28
Budget Start
2012-03-01
Budget End
2013-02-28
Support Year
4
Fiscal Year
2012
Total Cost
$302,851
Indirect Cost
$106,831
Name
University of California San Diego
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
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
Degner, Stephanie C; Verma-Gaur, Jiyoti; Wong, Timothy P et al. (2011) CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc Natl Acad Sci U S A 108:9566-71
Lucas, Joseph S; Bossen, Claudia; Murre, Cornelis (2011) Transcription and recombination factories: common features? Curr Opin Cell Biol 23:318-24
Mercer, Elinore M; Lin, Yin C; Murre, Cornelis (2011) Factors and networks that underpin early hematopoiesis. Semin Immunol 23:317-25
Lin, Yin C; Jhunjhunwala, Suchit; Benner, Christopher et al. (2010) A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol 11:635-43
Jhunjhunwala, Suchit; van Zelm, Menno C; Peak, Mandy M et al. (2009) Chromatin architecture and the generation of antigen receptor diversity. Cell 138:435-48