Every known nuclear regulatory event that occurs on the genome appears to be associated with a change in chromatin structure. Regulatory sequences that specify transcription, replication, DNA repair and recombination are located in regions whose structure changes with regulated function of these elements. The goal of this application is to devise technology that will allow chromatin structure to be examined over very large (100 kb or greater) regions of the genome. The focus is on mapping cleavage sites for chemicals and enzymes whose activity is known to display sensitivity to changes in chromatin structure. Development of this technology will not only provide an important, largely unbiased, mechanism for searching for novel regulatory elements, but will also provide a tool to increase the understanding of long-range changes in chromatin structure. There is precedent for the utility of mapping of cleavage sites in understanding gene regulation; for example the mapping of DNase hypersensitive sites has played a significant role in understanding promoter, enhancer and LCR function. A systematic, automated mapping of cleavage sites over regions of the genome an order of magnitude larger than those examined previously will prove to be a useful tool in both identification of regulatory elements and formation of hypotheses concerning the regulation of higher order chromatin structures. ? ? The following Aims will be pursued to develop a technology for long-range high-throughput mapping of cleavage sites:
Aim 1 will develop a single tube protocol for mapping cleavage sites in single copy mammalian DNA and will automate that protocol;
Aim 2 will apply the technology developed in Aim 1 to mapping large (up to 120 kb) regions of the mouse genome both in an undifferentiated multipotent stem cell line and in a homogeneous differentiated population of cells derived from that stem cell line.
Aim 3 will develop bioinformatics tools to interpret the data collected in Aim 2. ? ?

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
3R01HG003141-03S1
Application #
7124904
Study Section
Special Emphasis Panel (ZHG1)
Program Officer
Good, Peter J
Project Start
2003-09-30
Project End
2007-08-31
Budget Start
2005-09-01
Budget End
2007-08-31
Support Year
3
Fiscal Year
2005
Total Cost
$8,278
Indirect Cost
Name
Massachusetts General Hospital
Department
Type
DUNS #
073130411
City
Boston
State
MA
Country
United States
Zip Code
02199
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Woo, Caroline J; Kharchenko, Peter V; Daheron, Laurence et al. (2013) Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Mol Cell Biol 33:3274-85
Woo, Caroline J; Kharchenko, Peter V; Daheron, Laurence et al. (2010) A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell 140:99-110
Dennis, Jonathan H; Fan, Hua-Ying; Reynolds, Sheila M et al. (2007) Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res 17:928-39