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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Carter, Anthony D
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University of Massachusetts Medical School Worcester
Schools of Medicine
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Chou, Hsin-Jung; Donnard, Elisa; Gustafsson, H Tobias et al. (2017) Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. Mol Cell 68:978-992.e4
Vasseur, Pauline; Tonazzini, Saphia; Ziane, Rahima et al. (2016) Dynamics of Nucleosome Positioning Maturation following Genomic Replication. Cell Rep 16:2651-2665
Weiner, Assaf; Hsieh, Tsung-Han S; Appleboim, Alon et al. (2015) High-resolution chromatin dynamics during a yeast stress response. Mol Cell 58:371-86
Friedman, Nir; Rando, Oliver J (2015) Epigenomics and the structure of the living genome. Genome Res 25:1482-90
Rege, Mayuri; Subramanian, Vidya; Zhu, Chenchen et al. (2015) Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 13:1610-22
Hughes, Amanda L; Rando, Oliver J (2015) Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo. G3 (Bethesda) 5:1889-97
Hsieh, Tsung-Han S; Weiner, Assaf; Lajoie, Bryan et al. (2015) Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell 162:108-19
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 6:961-972
Chen, Hsiuyi V; Rando, Oliver J (2013) Painting by numbers: increasing the parts list for chromatin domains. Mol Cell 49:620-1
Möbius, Wolfram; Osberg, Brendan; Tsankov, Alexander M et al. (2013) Toward a unified physical model of nucleosome patterns flanking transcription start sites. Proc Natl Acad Sci U S A 110:5719-24

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