The DNA in the nucleus is complexed with proteins to form chromatin and chromatin domains of variable accessibility reside in specific regions of the nucleus. This packaging and organization is important for normal chromosomal processes like transcription and disruption of this organization is known to lead to developmental defects and disease states. The overall objective of this proposal is to reach a mechanistic understanding of the structure and organization of chromatin domains in eukaryotic chromosomes. DNA elements are necessary for the formation of chromatin domains and these elements also function to organize the domains within the three-dimensional context of the nucleus. Understanding long-range interactions between DNA elements and their role in the dynamics of chromatin domain is one focus of this proposal. The final goal is to understand how chromatin bound factors and DNA elements influence chromatin structure thereby affecting processes such as transcription. Adjacent chromatin domains in the nucleus often have antagonistic structural or functional properties and DNA insulator elements separate these domains. Promoters of specific genes often function as insulators in yeast and Drosophila and we have determined the broad outlines of the mechanisms by which these insulators function in yeast. In this grant we propose to investigate the changes that occur in chromatin domains as cells divide and to determine if similar mechanisms operate to separate chromatin domains in human cells. The research will involve use of molecular genetics and genomics, manipulation of chromatin using techniques like quantitative chromatin immunoprecipitations, and chromosome conformation capture and biochemical analysis. Understanding how the nucleus is organized should help us better manipulate processes for benefit in research. The results from this study will be useful in understanding the molecular basis of disease states that arise from mis-regulation of chromatin domains. The results will also enable researchers to develop new strategies for treating disease states by developing new molecular tools for gene therapy.

Public Health Relevance

Understanding how the nucleus is organized should help us better manipulate processes for benefit in research. The results from this study will be useful in understanding the molecular basis of disease states that arise from mis-regulation of chromatin domains. The results will also enable researchers to develop new strategies for treating disease states by developing new molecular tools for gene therapy.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM078068-08
Application #
8611927
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2007-03-01
Project End
2015-02-28
Budget Start
2014-03-01
Budget End
2015-02-28
Support Year
8
Fiscal Year
2014
Total Cost
$296,420
Indirect Cost
$91,420
Name
University of California Santa Cruz
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
125084723
City
Santa Cruz
State
CA
Country
United States
Zip Code
95064
Snider, Chloe E; Stephens, Andrew D; Kirkland, Jacob G et al. (2014) Dyskerin, tRNA genes, and condensin tether pericentric chromatin to the spindle axis in mitosis. J Cell Biol 207:189-99
Kirkland, Jacob G; Kamakaka, Rohinton T (2013) Long-range heterochromatin association is mediated by silencing and double-strand DNA break repair proteins. J Cell Biol 201:809-26
Kirkland, Jacob G; Raab, Jesse R; Kamakaka, Rohinton T (2013) TFIIIC bound DNA elements in nuclear organization and insulation. Biochim Biophys Acta 1829:418-24
Raab, Jesse R; Chiu, Jonathan; Zhu, Jingchun et al. (2012) Human tRNA genes function as chromatin insulators. EMBO J 31:330-50
Radman-Livaja, Marta; Ruben, Giulia; Weiner, Assaf et al. (2011) Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. EMBO J 30:1012-26
Ruben, Giulia J; Kirkland, Jacob G; MacDonough, Tracy et al. (2011) Nucleoporin mediated nuclear positioning and silencing of HMR. PLoS One 6:e21923
Kirkland, Jacob G; Kamakaka, Rohinton T (2010) tRNA insulator function: insight into inheritance of transcription states? Epigenetics 5:96-9
Raab, Jesse R; Kamakaka, Rohinton T (2010) Insulators and promoters: closer than we think. Nat Rev Genet 11:439-46
Valenzuela, Lourdes; Dhillon, Namrita; Kamakaka, Rohinton T (2009) Transcription independent insulation at TFIIIC-dependent insulators. Genetics 183:131-48
Dhillon, Namrita; Raab, Jesse; Guzzo, Julie et al. (2009) DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator. EMBO J 28:2583-600

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