DNA methylation is required for normal development of higher eukaryotes. Methylation is required for X-inactivation and genomic imprinting in mammals, and abnormal methylation is associated with cancer. In humans, mutation of a DNA methyltransferase (MTase) causes ICF syndrome and mutation of the methyI-DNA binding protein (MBP) MeCP2 causes Rett syndrome. DNA methylation is dispensable in the fungus Neurospora crassa, facilitating genetic studies. Isolation of Neurospora mutants defective in DNA methylation (dim) has led to insights into the control and function of methylation in eukaryotes. Most recently, identification of DIM-5 as a histone H3 MTase demonstrated that histone modifications control DNA methylation. The goal of the proposed research is to elucidate the mechanism of DNA methylation in eukaryotes by taking advantage of this outstanding model system. The work will be facilitated by valuable new resources and tools including: 1. the nearly complete sequence of the Neurospora genome, 2. A novel quelling-based system to recognize DNA methylation defects, 3. a mutagenic process, RIP (repeat-induced point mutation), for reverse-genetics, 4. antibodies specific for modified histones and 5. powerful new analytical methods (e.g., mass spectrometry and microarray analysis).
Specific aims of the project are: 1. To identify and genetically characterize proteins that bind methylated and RIP-mutated DNA (MRBP-1, MBP-2, MBP-3); 2. To characterize the DIM-2 DNA MTase, which is responsible for all detected methylation in vegetative cells, and the potential DNA MTase RID, which is required for RIP in sexual cells; 3. To carry out mutational analyses of the N-terminal tails of histones H4, H3, H2B and H2A to assess their role in DNA methylation in vivo; 4. To determine the role of histone methylation in DNA methylation; 5. To elucidate the role of histone acetylation and phosphorylation in DNA methylation; 6. To test the possible role of chromatin remodeling in DNA methylation; 7. To identify additional components of the DNA methvlation machinery.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Genetics Study Section (GEN)
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Carter, Anthony D
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University of Oregon
Schools of Arts and Sciences
United States
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Gessaman, Jordan D; Selker, Eric U (2017) Induction of H3K9me3 and DNA methylation by tethered heterochromatin factors in Neurospora crassa. Proc Natl Acad Sci U S A 114:E9598-E9607
Klocko, Andrew D; Ormsby, Tereza; Galazka, Jonathan M et al. (2016) Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa. Proc Natl Acad Sci U S A 113:15048-15053
Jamieson, Kirsty; Wiles, Elizabeth T; McNaught, Kevin J et al. (2016) Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome Res 26:97-107
Galazka, Jonathan M; Klocko, Andrew D; Uesaka, Miki et al. (2016) Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3. Genome Res 26:1069-80
Adhvaryu, Keyur K; Gessaman, Jordan D; Honda, Shinji et al. (2015) The cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora crassa. Eukaryot Cell 14:25-8
Klocko, Andrew D; Rountree, Michael R; Grisafi, Paula L et al. (2015) Neurospora importin ? is required for normal heterochromatic formation and DNA methylation. PLoS Genet 11:e1005083
Honda, Shinji; Lewis, Zachary A; Shimada, Kenji et al. (2012) Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol 19:471-7, S1
Belden, William J; Lewis, Zachary A; Selker, Eric U et al. (2011) CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet 7:e1002166
Selker, Eric U (2011) Neurospora. Curr Biol 21:R139-40
Anderson, D C; Green, George R; Smith, Kristina et al. (2010) Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa. Biochemistry 49:5244-57

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