Institute of Molecular Biology

Home

Faculty &
Research

Graduate
Admissions

Eric Selker

Professor of Biology

B.S., Reed College;
Ph.D., Stanford University

Institute of Molecular Biology

Office: Streisinger Hall Room 355D
Telephone: 541-346-5193

Lab: Streisinger Hall Room 355D
Telephone: 541-346-5197

Research Interests

DNA Methylation and Chromatin Modifications

We are interested in how the eukaryotic genome is structured, how it functions, and how it changes. Our current research is focused on gene silencing in eukaryotes. We are particularly interested in mechanisms involving special states of chromatin (e.g. heterochromatin)and DNA methylation. It is known that methylation alters properties of DNA, affects DNA-protein interactions, represses genes in animals, plants, and fungi and is essential for normal development in plants and mammals. Remarkably little is understood, however, about what determines which chromosomal regions are methylated. We are using genetic and biochemical approaches, with the filamentous fungus Neurospora crassa as a model, to elucidate the mechanism, control and function of DNA methylation and to explore other gene silencing systems.


Keyur Adhvaryu	Anthony Shiver

Zack Lewis	Francis Maddox

Tamir Khlafallah	Shinji Honda

Image courtesy of M. Springer and N. Raju

Image courtesy of A. Wolffe

One line of research involves identifying genes involved in DNA methylation. To date, we have identified five genes by mutagenesis and have isolated two that are essential for DNA methylation, dim-2 and dim-5. The former encodes a DNA methyltransferase responsible for all know methylation in the organism and the latter encodes a lysine9 histone H3 methyltransferase. We have confirmed that lysine9 of H3 plays a role in DNA methylation. This discovery indicates that DNA methylation takes its orders from chromatin. Additional studies in the laboratory are providing other insights into the workings of DNA methylation. For example, we have recently identified factors that specifically bind to methylated sequences and a protein that binds to sequences destined to be methylated. The recent availability of the nearly complete sequence of the Neurospora genome is allowing us to carry out "reverse-genetics" investigations of chromatin and DNA methylation in this model system.

Reactivation of hph and loss of DNA methylation induced by transformation of a dim⁺ strain with mutant alleles of histone H3 gene.

a. Sequence of N-terminal segment of Neurospora histone H3 with residues presumed to be subject to methylation(m), acetylation(a) or phosphorylation(p) in red and the residue implicated in silencing highlighted in yellow.
b. A strain bearing a silenced (methylated) hyg^R gene was co-transformed with a bml^R resistance gene and wildtype or mutant versions of the histone H3 gene, bml^R transformants were selected en masse on bml and tested for hyg^R.
c. Southern analysis and sequencing of DNAfrom hyg^R transformants. DNA of representative transformants(T) and a wildtype(wt) control was analyzed with EcoRI and BamHI for methylation(m) at 63 and for ectopic alleles of hH3.

Direct sequencing of hH3 PCR products confirmed the presence of both the wild type and mutant alleles in representative strains (sequencing chromatograms).

Repeat Induced Point (RIP) Mutation

Another line of research is directed at elucidating the mechanism of RIP (repeat-induced point mutation), a process that we discovered some time ago. During the sexual phase of the Neuropora life cycle, in the stage between fertilization and nuclear fusion, RIP efficiently detects duplicated DNA sequences (both linked and unlinked) and then modifies them by making G:C to A:T mutations. Cytosines remaining in a region mutated by RIP are typically methylated.

Inactivation of duplicated albino gene

Image courtesy of C. Staben

Inactivation of duplicated genes by RIP (hatch boxes) occurs prior to meiosis in Neuorspora.

Typical mutations and DNA methylation by RIP in a set of am^RIP alleles

Alleles 5-8 (red) trigger methylation de novo in vegetative cells; alleles 3 and 4 (blue) were methylated after RIP but do not trigger metylation de novo. Alleles 1 and 2 (black) were found unmethylated after RIP.

Selected Publications

Grimaldi, B., Coiro, P., Filetici, P., Berge, E., Dobosy, J.R., Freitag, M., Selker, E., and Ballario, P., (2006) The Neurospora crassa White Collar-1 dependent Blue Light Response Requires Acetylation of Histone H3 Lysine 14 by NGF-1 Mol Biol Cell, 17 (10): 4576-83

Galagan, J.E., Calvo, S.E., et al (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105-1115.

Allshire, R. and Selker, E.U. Fungal models for epigenetic research: Schizosaccharomyces pombe and Neurospora crassa. Chapter 6 in "Epigenetics", Edited by C. D. Allis, T. Jenuwein, D Reinberg. Cold Spring Harbor Laboratory Press, USA, in press.

Adhvaryu, K,, Morris, S., Strahl, B. D. and Selker, E. U. (2005) Methylation of histone H3 lysine 36 is essential for normal development in Neurospora crassa. Eukaryotic Cell, 4 (8):1455–1464.

Freitag M. and Selker E.U. (2005) Controlling DNA methylation: many roads to one modification. Current Opinion in Genetics & Development 15 (4) pp 191-99

Collins R.E., Tachibana M., Tamaru H., Smith K.M., Jia D., Zhang X., Selker E.U., Shinkai Y., Cheng X. (2005) In vitro and in vivo analyses of a phe/tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem 280:5563-70.

Freitag M., Hickey P.C., Raju N.B., Selker E.U., Read N.D. (2004) GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa. Fungal Genet Biol 41:897-910.

Galagan JE, Selker EU (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20:417-23.

Borkovich K.A., et al. (2004) Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism. Microbiol Mol Biol Rev 68:1-108.

Freitag M., P.C. Hickey, T.K. Khlafallah, N.D. Read, and E.U. Selker (2004) HP1 is essential for DNA methylation in neurospora Mol Cell 13:427-34.

Zhang X., Z. Yang, S.I. Khan, J.R. Horton, H. Tamaru, E.U. Selker, and X. Cheng (2003) Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell 12:177-85.

Selker E.U. (2003) Molecular biology. A self-help guide for a trim genome. Science 300:1517-8.

Selker E.U., N.A. Tountas, S.H. Cross, B.S. Margolin, J.G. Murphy, A.P. Bird, and M. Freitag (2003) The methylated component of the Neurospora crassa genome. Nature 422:893-7.

Galagan, J.E. et al (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-68.

Folco H.D., M. Freitag, A. Ramon, E.D. Temporini, M.E. Alvarez, I. Garcia, C. Scazzocchio, E.U. Selker, and A.L. Rosa (2003) Histone H1 Is required for proper regulation of pyruvate decarboxylase gene expression in Neurospora crassa. Eukaryot Cell 2:341-50.

Tamaru H., X. Zhang, D. McMillen, P.B. Singh, J. Nakayama, S.I. Grewal, C.D. Allis, X. Cheng, E.U. Selker (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34:75-9.

Tamaru H. and E.U. Selker (2003) Synthesis of signals for de novo DNA methylation in Neurospora crassa. Mol Cell Biol 23:2379-94.

Cheng, J.C., C.B. Matsen, F.A. Gonzales, S. Greer, V.E. Marquez, P.A. Jones, and E.U. Selker (2003) Zebularine is an inhibitor of DNA methylation with clinical promise. J Natl Cancer Inst 95:399-409.

Zhang, X., H. Tamaru, S.I. Khan, J.R. Horton, L.J. Keefe, E.U. Selker, and X. Cheng (2002) Structure of the Neurospora SET Domain Protein DIM-5, a Histone H3 Lysine Methyltransferase. Cell 111:117-27.

Selker, E.U., M. Freitag, G.O. Kothe, B.S. Margolin, M.R. Rountree, C.D. Allis, and H. Tamaru (2002) Induction and maintenance of nonsymmetrical DNA methylation in Neurspora. PNAS Aug 20 [epub].

Freitag, M., R.L. Williams, G.O. Kothe, and E.U. Selker (2002) A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. PNAS 99:8802-7.

Selker, E.U. (2002) Repeat-induced gene silencing in fungi. Adv Genet 46:439-50.

Hays, S.M., J. Swanson, and E.U. Selker (2002) Identification and Characterization of the Genes Encoding the Core Histones and Histone Variants of Neurospora crassa. Genetics 160:961-73.

Tamaru, H. and E.U. Selker (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277-83.

Kouzminova E. and E.U. Selker (2001) dim-2 encodes a DNA methyltransferase responsible for all know cytosine methylation in Neurospora. EMBO J 20:4309-23.

Dobosy J.R. and E.U. Selker (2001) Emerging connections between DNA methylation and histone acetylation. Cell Mol Life Sci 58:721-7.

Miao V.P., M. Freitag, and E.U. Selker (2000) Short TpA-rich segments of the zeta-eta region induce DNA methylation in Neurospora crassa. J Mol Biol 300:249-73.

Selker, E.U. (1999) Gene silencing: Repeats that count. Cell 97:157-60.

Margolin, B.S., P.W. Garrett-Engele, J.N. Stevens, D. Yen-Fritz, C. Garrett-Engele, R.L. Metzenberg, and E.U. Selker (1998) A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by Repeat-Induced Point Mutation. Genetics 149:1787-97.

Selker, E.U. (1998) Trichostatin A causes selective loss of DNA methylation in Neurospora. PNAS 95:9430-5.

Selker, E.U. (1997) Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends in Genetics 13:296-301.

Rountree, M.R. and E.U. Selker (1997) DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes and Development 11:2383-95.

Perkins, D.D., B.S. Margolin, E.U. Selker, and S.D. Haedo (1997) Occurrence of repeat induced point mutation in long segmental duplications of Neurospora. Genetics 147:125-36.

Irelan, J.T. and E.U. Selker (1997) Cytosine methylation associated with repeat-induced point mutation (RIP) causes epigenetic gene silencing in Neurospora crassa. Genetics 146:509-23.

Cogoni, C., J.T. Irelan, M. Schumacher, T. Schmidhauser, E.U. Selker, and G. Macino (1996) Transgene silencing of the al-2 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA:DNA interactions or DNA methylation. EMBO J 15:3153-63.

Cambareri, E.B., H.M. Foss, M.R. Rountree, E.U. Selker, and John A. Kinsey (1996) Epigenetic regulation of a transposon-inactivated gene in Neurospora is dependent on DNA methylation. Genetics 143:137-46.

Singer, M.J., B.A. Marcotte, and E.U. Selker (1995) DNA methylation associated with repeat-induced point mutation (RIP) in Neurospora crassa. Mol Cell Biol 15:5586-97.

Miao, V.P.W., M.R. Rountree, and E.U. Selker (1995) Ectopic integration of transforming DNA is rare among Neurospora transformants selected for gene replacement. Genetics 139:1533-44.

Kinsey, J.A., P.W. Garrett-Engele, E.B. Cambareri, and E.U. Selker (1994) The Neurospora transposon Tad is sensitive to repeat-induced point mutation (RIP). Genetics 138:657-64.

Selker, E.U., G.A. Richardson, P.W. Garrett-Engele, M.J. Singer, and V. Miao (1993) Dissection of the signal for DNA methylation in the zeta-eta region of Neurospora. Cold Spring Harbor Symposia on Quantitative Biology 58:323-9.

Selker, E.U., D.Y. Fritz, and M.J. Singer (1993) Dense non-symmetrical DNA methylation resulting from repeat-induced point mutation (RIP) in Neurospora. Science 262:1724-8.

Selker, E.U. (1990) Premeiotic instability of repeated sequences in Neurospora crassa. Annual Review of Genetics 24:579-613.

IMB Home | Department of Physics | Department of Chemistry
Department of Biology | UO Life Sciences | University of Oregon

Institute of Molecular Biology
297 Klamath Hall Hall, 1229 University of Oregon, Eugene, OR 97403-1229
Telephone: 541-346-5151 Fax: 541-346-5891