Cytosine DMA methylation is an epigenetic mark for gene silencing that is important in many gene regulatory systems including genomic imprinting, X-chromosome inactivation, and the silencing of transposons and other DNA sequences containing either direct or inverted repeats. Methylation is important in cancer biology, as tumors often show both genome wide demethylation and hypermethylation of specific tumor suppressor genes. We are studying the mechanisms of DNA methylation control in the model plant Arabidopsis thaliana. Arabidopsis DNA methylation systems have much in common with mammalian systems, showing homologs of the three human DNA methyltransferases, Dnmtl, 2, and 3. Both forward and reverse genetics can be performed, and Arabidopsis can tolerate mutations that virtually eliminate methylation, allowing for detailed analysis. We have recently discovered that RNA silencing components including a DICER, an RNA-dependent RNA polymerase, and an ARGONAUTE protein, are central to the mechanisms by which DNA methylation is established, and by which methylation in non-CG contexts is maintained. We propose a series of genetic and biochemical experiments to further study this phenomena. Direct repeats and inverted repeats can trigger de novo DNA methylation by different mechanisms, and we propose to study these differences. We also propose mutant screens aimed at isolating factors important in these processes. The ARGONAUTE4 protein likely acts at the interface between small RNAs and chromatin modifying enzymes, and we propose to study the mechanism of action of this protein in detail. Since many aspects of DNA methylation control mechanisms are similar in diverse eukaryotic organisms, it is likely that progress made in Arabidopsis will shed light on a wide array of epigenetic regulatory systems involved in genome defense, developmental biology, and human disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM060398-09
Application #
7332246
Study Section
Genetics Study Section (GEN)
Program Officer
Carter, Anthony D
Project Start
2000-01-01
Project End
2008-12-31
Budget Start
2008-01-01
Budget End
2008-12-31
Support Year
9
Fiscal Year
2008
Total Cost
$257,069
Indirect Cost
Name
University of California Los Angeles
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
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Zhang, Yu; Harris, C Jake; Liu, Qikun et al. (2018) Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proc Natl Acad Sci U S A 115:E1069-E1074
Feng, Wei; Hale, Christopher J; Over, Ryan S et al. (2017) Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage. Proc Natl Acad Sci U S A 114:406-411
Weiser, Natasha E; Yang, Danny X; Feng, Suhua et al. (2017) MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality. Dev Cell 41:408-423.e7
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Groth, Martin; Moissiard, Guillaume; Wirtz, Markus et al. (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun 7:11640
Li, Sisi; Yang, Zhenlin; Du, Xuan et al. (2016) Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette. Structure 24:486-94
Lahmy, Sylvie; Pontier, Dominique; Bies-Etheve, Natacha et al. (2016) Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes Dev 30:2565-2570

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