Cytosine methylation is a DNA modification found in the genomes of eukaryotes including mammals, higher. plants, and filamentous fungi. Methylation is associated with loss of gene expression (silencing) and suppression of homologous recombination. Maintenance of correct methylation patterns is critically important for development. For example, in humans, alteration of methylation patterns in certain genomic regions leads to a number of genetic diseases including mental retardation syndromes and pre-disposition to malignancies. In mice, a cytosine methyltransferase knock-out mutation results in embryo-lethality. In the higher plant model organism Arabidopsis thaliana, methylation-deficient mutants display a number of aberrant morphologies but are nonetheless viable and fertile. Therefore, Arabidopsis provides an extremely tractable system to study the mechanisms of methylation and silencing with molecular and genetic approaches. Our research focuses on a family of methylated endogenous genes in Arabidopsis that consists of two singlet genes plus a tail-to-tail inverted repeat gene duplication at three unlinked genomic positions. Previous work showed that the inverted repeat locus triggers methylation of the identical sequences elsewhere in the genome. Paradoxically, although methylation causes silencing of a singlet locus, a gene in the methylated inverted repeat is expressed. The goal of this proposal is to understand the mechanisms by which the inverted repeat locus escapes the normally repressive effects of methylation. This question will be explored by characterizing the chromatin structure, cis-acting DNA sequences, and trans-acting factors that control methylation and expression of the silenced singlet locus versus the expressed inverted repeat locus.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM061148-03
Application #
6520219
Study Section
Genetics Study Section (GEN)
Program Officer
Carter, Anthony D
Project Start
2000-07-01
Project End
2004-06-30
Budget Start
2002-07-01
Budget End
2003-06-30
Support Year
3
Fiscal Year
2002
Total Cost
$249,338
Indirect Cost
Name
Johns Hopkins University
Department
Biochemistry
Type
Schools of Public Health
DUNS #
045911138
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