The packaging of eukaryotic genomes into chromatin affects DNA-templated processes from transcription to recombination, but we still lack a deep understanding of how chromatin structure even affects transcriptional regulation. Chromatin regulators are widely implicated in human cancers and other diseases and are attractive drug targets, making chromatin structure and function a key goal for modern molecular biology and medicine. Much of our understanding of chromatin function comes from relatively static studies in a single growth condition. Over the first five years of this grant, my laboratory has extended typical static genomic chromatin assays to dynamic contexts, revealing a great deal of novel biology that can only be appreciated when cells are not under steady-state conditions. Here, we plan to focus on chromatin dynamics at two different time scales. The first project concerns changes in chromatin structure during changes in transcription, and the role for chromatin in transcriptional control. Classic studies on model genes reveal that many chromatin regulators do not affect steady-state mRNA production, but rather affect the rate of gene induction or repression in response to environmental signals. By carrying out genome-scale gene expression analysis in hundreds of chromatin mutants subjected to a stress response, coupled with genome-wide mapping of chromatin structural transitions under the same conditions, we propose to systematically dissect histone modification pathways in yeast. The second project concerns changes in chromatin structure during the cell cycle and the capacity of chromatin to serve as epigenetic memory. Our prior measurements on histone dynamics across multiple cell cycles suggest that histones spread up to ~400 bp during genomic replication. This measurement has key implications for the fidelity with which chromatin states may be inherited, as it would limit potential epigenetic inheritance of chromatin domains to those ~1 kb or larger. We propose to independently measure the movement of histone proteins during genomic replication, and to separately characterize histone dynamics on the leading and lagging strand genomes. Finally, we will determine whether ancestral histone accumulation can affect gene regulation. Together, our studies provide a broad-based investigation into chromatin structural dynamics during transcription and across multiple cell cycles, and will provide an improved framework for understanding the function of chromatin in gene regulation and epigenetic inheritance.

Public Health Relevance

The packaging of eukaryotic genomes into chromatin affects DNA-templated processes from transcription to recombination, and chromatin regulators are widely implicated in human cancers and other diseases and therefore are attractive drug targets. The majority of studies on chromatin structure and function are carried out in steady-state conditions, thereby missing key roles for chromatin in dynamic processes such as gene induction/repression or epigenetic inheritance. In this proposal we will extend our studies on chromatin dynamics to study the role of chromatin regulators in transcription reprogramming, and the role of ancestral histone accumulation in epigenetic gene regulation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM079205-06
Application #
8437421
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Carter, Anthony D
Project Start
2008-03-01
Project End
2017-02-28
Budget Start
2013-03-08
Budget End
2014-02-28
Support Year
6
Fiscal Year
2013
Total Cost
$433,092
Indirect Cost
$172,306
Name
University of Massachusetts Medical School Worcester
Department
Biochemistry
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
Soares, Luis M; Radman-Livaja, Marta; Lin, Sherry G et al. (2014) Feedback control of Set1 protein levels is important for proper H3K4 methylation patterns. Cell Rep 6:961-72
Watanabe, Shinya; Radman-Livaja, Marta; Rando, Oliver J et al. (2013) A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme. Science 340:195-9
Tsankov, Alex; Yanagisawa, Yoshimi; Rhind, Nicholas et al. (2011) Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 21:1851-62
Sikorski, Timothy W; Ficarro, Scott B; Holik, John et al. (2011) Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell 44:397-409
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
Lopes da Rosa, Jessica; Holik, John; Green, Erin M et al. (2011) Overlapping regulation of CenH3 localization and histone H3 turnover by CAF-1 and HIR proteins in Saccharomyces cerevisiae. Genetics 187:9-19
Rando, Oliver J (2011) Genome-wide measurement of histone H3 replacement dynamics in yeast. Methods Mol Biol 759:41-60
Papamichos-Chronakis, Manolis; Watanabe, Shinya; Rando, Oliver J et al. (2011) Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell 144:200-13
Ivanovska, Iva; Jacques, Pierre-Etienne; Rando, Oliver J et al. (2011) Control of chromatin structure by spt6: different consequences in coding and regulatory regions. Mol Cell Biol 31:531-41
Radman-Livaja, Marta; Verzijlbergen, Kitty F; Weiner, Assaf et al. (2011) Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol 9:e1001075

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