Professor of Biology
B.S., Reed College;
Ph.D., Stanford University
Member of: Institute of Molecular Biology
Office: Streisinger Hall Room 355D
Lab: Streisinger Hall Room 355D
- Control and Function of DNA Methylation in Eukaryotes
- Chromatin Structure and Function
Figure 1. The filamentous fungus Neurospora crassa.
Image courtesy of M. Springer and N. Raju
We are interested in how the eukaryotic genome is structured, how it functions, and how it changes. Our current research concentrates on gene silencing in eukaryotes. We are particularly interested in mechanisms involving special states of chromatin (e.g. heterochromatin) and DNA methylation. 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, primarily with the filamentous fungus Neurospora crassa (Fig. 1) as a model, to elucidate the mechanism, regulation and function of DNA methylation. In addition, we are using these approaches to explore silencing associated with chromosome ends, centromeres and other specialized regions of the genome.
Figure 2. Inactivation of duplicated genes by RIP (shading) occurs prior to meiosis in Neurospora (see: Selker 1990 Ann. Rev. Gen. 24, 579-613).
DNA methylation is essential for normal development in a wide range of organisms including mammals and plants but is absent in some organisms including many popular model eukaryotes (e.g., yeasts, Drosophila, C. elegans). We showed that ~2% of cytosines in Neurospora DNA are methylated and that DNA methylation is not essential for development or viability in this organism. This set the stage for us to exploit this model eukaryote to elucidate the control and function of DNA methylation.
We found that most methylated regions of Neurospora are relics of transposons inactivated by RIP (repeat-induced point mutation), a premeiotic homology-based genome defense system that litters duplicated sequences with C:G to T:A mutations (Figs. 2 & 3).
Figure 3. Detailed analyses of DNA methylation in the Neurospora genome revealed that it is mostly in AT-rich centromeric regions, subtelomeric regions and dispersed relics of RIP, as shown here in red for one chromosome (see Lewis et al. 2008 Genome Research 19, 427-437).
Our genetic and biochemical studies on the control of DNA methylation revealed clear ties between DNA methylation and chromatin modifications. The DIM-2 DNA methyltransferase is directed by heterochromatin protein 1 (HP1), which in turn recognizes trimethyl-lysine 9 on histone H3, placed by the DIM-5 histone H3 methyltransferase (Fig. 4).
Figure 4. Localization of HP1-GFP depends on H3K9m3 by DIM-5. Note that the foci of heterochromatin in nuclei of wildtype are lost in the dim-5 mutant. (see Freitag M et. Al. 2004 Mol Cell 13, 427-34.)
DNA methylation is modulated by a variety of additional factors. For example, in dmm-1 (DNA methylation modulator-1) mutants, methylation spreads from inactivated transposable elements, which can silence adjacent genes and lead to poor growth. Additional studies in the laboratory are providing other insights into the workings of DNA methylation and other silencing processes.
Figure 5. Heterochromatin formation and DNA methylation. DIM-7 recruits the DIM-5 histone methyltransferase to A:T rich DNA (red), to form DCDC (Dim-Cul4-DDB1 Complex) resulting in methylation of K9 of histone H3. HP-1 then recognizes this histone mark and recruits the DIM-2 DNA methyltransferase (see Lewis et al. 2010. PLoS Genetics 6, e1001196).
|Kirsty Jamieson||Mike Rountree||Paula Grisafi|
|Andy Klocko||Robert Parrish||Tereza Ormsby|
|Kevin McNaught||Jordan Gessaman||Vince Bicocca|
|Calvin Summers||Tish T. Wiles|
Jamieson et al. (2013) Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci USA Vol. 110: 6027-6032.
Qi, X., Li, Y., Honda, S., Hoffmann, S., Marz, M., Mosig, A., Podlevsky, J.D, Stadler, P.F, Selker, E.U. and Chen, J. J-L. (2012) The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Research doi:10.1093/nar/gks980 pp. 1-13
Honda, S., Lewis, S.A., Shimada, K., Fischle, W., Sack, R. and Selker, E.U. (2012) HP1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nature Structural and Molecular Biology. Nature Structural and Molecular Biology. 19, 471-477.
Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC (2011) CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet 7(7): e1002166.
Selker. Neurospora. Curr Biol (2011) vol. 21 (4) pp. R139-R140.
Adhvaryu, K.K., Berge, E., Tamaru, H., Freitag, M., and Selker, E.U. (2011) Substitutions in theamino-terminal tail of Neurospora histone H3 have varied effects on DNA methylation. PLoS Genet 7(12): e1002423.
Smith, K.M, Dobosy, J.R., Reifsnyder, J.E., Rountree, M.R., Anderson, D.C, Green, G.R., and Selker, E.U. (2010) H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa. Genetics 186, 1207-1216
Lewis, Z.A., Adhvaryu, K.K., Honda, S., Shiver, A.L, Knip, M., Sack, R. and Selker, E.U. (2010) DCDC, a DIM-5/-7/-9/CUL4/DDB1 Protein Complex, is Essential for DNA Methylation in Neurospora. PloS Genetics 6, e1001196.
Anderson DC, Green GR, Smith K, Selker EU. (2010) Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa. Biochemistry. Jun 29;49(25):5244-57.
Xiong L, Adhvaryu KK, Selker EU, Wang Y. (2010) Mapping of lysine methylation and acetylation in core histones of Neurospora crassa. Biochemistry. Jun 29;49(25):5236-43.
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y. (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell. Jun 25;38(6):803-14.
Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU. (2010) Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. Proc Natl Acad Sci U S A. May 4;107(18):8310-5.
Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU. (2010) The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes Dev. Mar 1;24(5):443-54.
Wu, C., Kim, Y-S., Smith, K.M., Li, W., Hood, H.M., Staben, C., Selker, E.U., Sachs, M.S., and Farman M.L. (2009) Characterization of chromosome ends in the filamentous fungus Neurospora crassa. Genetics 181: 1129-1145.
Honda, S. and Selker, E.U. (2009) Tools for fungal proteomics: Multifunctional Neurospora vectors for gene replacement, protein expression and protein purification. Genetics 182: 11-23.
Selker, E.U. (2008) Robert L. Metzenberg, June 11, 1930-July 15, 2007: Geneticist extraordinaire and “Model Human”. Genetics 178, 611-619.
Lewis, Z.A. Honda, S., Khlafallah, T.K. Jeffress, J.K., Freitag, M., Mohn, B., Schübeler, D. and Selker, E.U. (2008) Relics of repeat-induced point mutation direct heterochromatin in Neurospora crassa. Genome Research 19: 427-437.
Smith, K.M., Kothe, G.O., Matsen, C.B., Khlafallah, T.K., Adhvaryu, K.K., Hemphill, M. Freitag, M., Motamedi, M.R. and Selker, E.U. (2008) The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9. Epigenetics and Chromatin 1(1): 5
Adhvaryu, K.K. and Selker, E.U. (2008) Protein phosphatase PP1 is required for normal DNA methylation in Neurospora. Genes and Development, 22:3391–3396
Lee, D.W., Freitag, M., Selker, E.U. and Aramayo, R. (2008) A cytosine methyltransferase-like is essential for sexual development in Aspergillus nidulans. PLoS ONE 3: e2531.
Honda, S. and Selker, E.U. (2008) Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora. Mol. Cell. Biol. 28(19):6044-55
Perkins, D.D., Freitag, M., Pollard, V.C., Bailey-Shrode, L.A., Selker, E.U. and Ebbole, D.J. (2007) Recurrent locus-specific mutation resulting from a cryptic ectopic insertion in Neurospora. Genetics, 175: 527-44
Allshire, R. and Selker, E.U. (2007) Fungal models for epigenetic research: Schizosaccharomyces pombe and Neurospora crassa. pages 101-125 in "Epigenetics", Edited by C. D. Allis, T. Jenuwein, D Reinberg. Cold Spring Harbor Laboratory Press.
Lewis, Z.A., Shiver, A., Stiffler, N., Miller, M.R., Johnson, E.A., and Selker, E.U. (2007) High density detection of restriction site associated DNA (RAD) markers for rapid mapping of mutated loci in Neurospora. Genetics 177: 1163-71.
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
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.
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.
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.