In eukaryotes including mammals and plants, cytosine methylation and associated heterochromatin formation play a key role in regulating gene expression and genome integrity. Dysregulation of cytosine methylation contributes to human cancers and a number of genetic disorders. Cytosine methylation is also critical for the suppression of transposon expression and movement. We use a group of duplicated methylated endogenous genes in the laboratory plant Arabidopsis as a model system to study the establishment and maintenance of cytosine methylation and gene silencing. In this system, the methylation imprint is established by a double-stranded RNA (dsRNA)-based signal. This mode of methylation targeting was first elucidated in plants, but it is now clear that related mechanisms for RNA-directed heterochromatin formation occur in fungi and animals including mammals. As one aim of this proposal, we will further characterize the RNA signal for DMA methylation using a combination of genetic studies with RNA processing/binding mutants and molecular analysis of RNA, with a focus on understanding the role of short interfering RNAs (siRNAs) in guiding methylation patterning. As a second aim, we will use a novel genetic screen for factors that specifically maintain methylation at a dsRNA source locus. We have also determined that key factors for maintaining the RNA-directed DNA methylation imprint are a cytosine methyltransferase CMT3 and a histone H3 lysine 9 (K9) methyltransferase SUVH4/KYP. This relationship between cytosine methylation and histone H3 K9 methylation also occurs in fungal and mammlian systems. In the third aim of this proposal, we will characterize the stucture and function of SUVH4/KYP and partially redundant related SUVH proteins using biochemical, genetic, and transgenic approaches, with the long-term goal of understanding the connections between RNA, histone methylation, and DNA methylation. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM061148-06
Application #
7114978
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2000-07-01
Project End
2007-08-31
Budget Start
2006-09-01
Budget End
2007-08-31
Support Year
6
Fiscal Year
2006
Total Cost
$300,310
Indirect Cost
Name
Johns Hopkins University
Department
Biochemistry
Type
Schools of Public Health
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Enke, Raymond A; Dong, Zhicheng; Bender, Judith (2011) Small RNAs prevent transcription-coupled loss of histone H3 lysine 9 methylation in Arabidopsis thaliana. PLoS Genet 7:e1002350
Johnson, Mark A; Bender, Judith (2009) Reprogramming the epigenome during germline and seed development. Genome Biol 10:232
Mull, Lori; Ebbs, Michelle L; Bender, Judith (2006) A histone methylation-dependent DNA methylation pathway is uniquely impaired by deficiency in Arabidopsis S-adenosylhomocysteine hydrolase. Genetics 174:1161-71
Ebbs, Michelle L; Bender, Judith (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18:1166-76
Ebbs, Michelle L; Bartee, Lisa; Bender, Judith (2005) H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 25:10507-15
Melquist, Stacey; Bender, Judith (2004) An internal rearrangement in an Arabidopsis inverted repeat locus impairs DNA methylation triggered by the locus. Genetics 166:437-48
Bender, Judith (2004) Chromatin-based silencing mechanisms. Curr Opin Plant Biol 7:521-6
Melquist, Stacey; Bender, Judith (2003) Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev 17:2036-47
Malagnac, Fabienne; Bartee, Lisa; Bender, Judith (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21:6842-52
Bartee, L; Malagnac, F; Bender, J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15:1753-8