Eukaryotic chromatin fibers are folded into topologically independent loop domains in interphase nuclei. This is thought to be accomplished by chromatin making periodic attachments to the residual framework of nuclei, called the nuclear matrix, at specialized DNA sequences called matrix attachment regions, or MARs. Such higher order chromatin structure might have both structural and functional significance in gene regulation. We have previously cloned a cell-type specific MAR-binding protein, SATB 1, which is expressed in thymocytes and activated T cells. SATBI coordinates multiple genes in the T cell lineage. Using SATB1 as a tool to isolate MARS, we have identified a series of SATB1-binding fragments from the -1 megabase mouse cytokine gene cluster region at chomosome 11 as putative MARs. In this proposal, we propose to 1) identify and map all potential MARs within this locus by both biochemical and computational methods, and characterize each MAR by delineating the key structural element (base unpairing region: BUR), which is typically found in MARs, 2) similarly screen for MARs in the human cytokine gene cluster region at chromosome 5q31 and identify BURs that are found in the syntenic region of the mouse chromosome 11, 3) determine which of these BURs make attachment to the nuclear matrix in T cells at different differentiation stages and examine their in vivo binding status to SATB1, and 4) examine the biological function of selected BURs by establishing BUR-deleted mice. In these mice, we will examine the effects of BUR deletion on the specific loop organization of chromatin, T cell differentiation-specific gene expression, and local chromatin structure including the methylation status. The research proposed here will test whether certain BURs can act as long-range regulatory elements by forming a specific loop domain structure during T cell differentiation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM063026-04
Application #
6788842
Study Section
Cell Development and Function Integrated Review Group (CDF)
Program Officer
Carter, Anthony D
Project Start
2001-09-01
Project End
2006-08-31
Budget Start
2004-09-01
Budget End
2006-08-31
Support Year
4
Fiscal Year
2004
Total Cost
$222,945
Indirect Cost
Name
Lawrence Berkeley National Laboratory
Department
Type
Organized Research Units
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720