Department of Biology  |  Institute of Molecular Biology

University of Oregon

SELECTED PUBLICATIONS:

 

 

Klocko, A.D., Uesaka, M., Ormsby, T., Rountree, M.R., Wiles, E.T., Adhvaryu, K.K., Honda, S. and Selker, E.U. (2019) Nucleosome positioning by DIM-1 prevents aberrant DNA methylation in Neurospora. Genetics in press.

 

Bicocca, V.T., Ormsby, T., Adhvaryu, K.K. Keyur K. Adhvaryu, Honda, S. and Selker, E.U. (2018) ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin. eLife 7:e41497.

 

Jamieson, K., McNaught, K.J., Ormsby, T., Leggett, N.A., Honda, S. and Selker, E.U. (2018) Telomere repeats induce domains of H3K27 methylation in Neurospora.  eLife, 7:e31216.

 

Gessaman, J.D. and Selker, E.U. (2017) Induction of H3K9me3 and DNA methylation by tethered heterochromatin factors in Neurospora crassa. Proc. Natl. Acad. Sci. USA.  10.1073/pnas.1715049114.

 

Klocko, A.D., Ormsby, T., Galazka, J.M., Leggett, N., Uesaka, M., Honda, S. Freitag, M. and Selker, E.U. (2016)  Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa. Proc Natl Acad Sci U S A. 113: 15048–15053.

 

Wiles E.T. and Selker, E.U. (2016) H3K27 methylation: A promiscuous repressive chromatin mark. Current Opinion in Genetics & Development 43: 31–37.

 

Honda S, Bicocca VT, Gessaman JD, Rountree, M.R., Yokoyama, A., Yu, Eun Y., Selker, J.M.L. and Selker, E.U. (2016). Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa. Proc Natl Acad Sci U S A. www.pnas.org/cgi/doi/10.1073/pnas.1614279113.

 

Galazka, J.M., Klocko, A.D., Uesaka, M., Honda, S., Selker, E.U. and Freitag, M. (2016) Neurospora chromosomes are organized by blocs of importin α-dependent heterochromatin that are largely independent of H3K9me3. Genome Research, 26: 1069-1080.

 

Jamieson, K., Wiles E.T., McNaught, K.J., Sidoli, S., Leggett, N., Shao, Y., Garcia, B.A. and Selker, E.U.  (2016) Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin.  Genome Research 26: 97-107.

 

Klocko, A.D, Rountree, M.R., Grisafi, P.L., Hays, S.M., Adhvaryu K.K. and Selker, E.U. (2015) Neurospora Importin  is Required for Normal Heterochromatic Formation and DNA Methylation. PLoS Genetics 11, e1005083.

 

Adhvaryu K.K., Gessaman, J.D., Honda, S., Lewis, Z.A., Grisafi, P.L., Selker, E.U. (2015)  The Cullin-4 Complex DCDC Does Not Require E3 Ubiquitin Ligase Elements To Control Heterochromatin in Neurospora crassa. Eukaryotic Cell 14: 25-28.

 

Aramayo, R. and Selker, E.U. (2013)  Neurospora crassa, a Model System for Epigenetic Research.  Cold Spring Harb Perspect Biol 2013;5:a017921.

 

Jamieson, K., Rountree, M.R., Lewis, Z.A., Stajich, J.E. and Selker, E.U. (2013) Regional control of histone H3 lysine 27 methylation in Neurospora.  Proc Natl Acad Sci U S A 110: 6027-6032.

 

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. 19:  471-477.

 

Adhvaryu, K.K., Berge, E., Tamaru, H., Freitag, M., and Selker, E.U. (2011) Substitutions in the amino-terminal tail of Neurospora histone H3 have varied effects on DNA methylation.  PLoS Genet 7(12): e1002423.

 

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.

 

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) DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC. PLoS Genet 6(11): e1001196.

 

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. Molecular Cell 38: 803-14.

 

Lewis, Z.A., Adhvaryu, K.K., Honda, S., Shiver, A.L., and Selker, E.U. (2010) Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin. Proc Natl Acad Sci U S A 107:  8310-8315.

 

Honda, S., Lewis, Z.A., Huarte, M., Cho, L.Y., David, L.L., Shi, Y., and Selker, E.U. (2010) The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa. Genes and Development 24: 443-454.

 

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.

 

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.

 

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.

 

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: 6044-55.

 

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.  Euk. Cell 4: 1455–1464.

 

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., Lee, D.W., Kothe, G.O., Pratt, R.J., Aramayo, R. and Selker, E.U. (2004) DNA methylation is Independent of RNA Interference in Neurospora.  Science 304: 1939.

 

Freitag, M., Hickey, P.C, Khlafallah, T.K, Read, N.D. and Selker, E.U.  (2004) HP1 is essential for DNA methylation in Neurospora. Mol. Cell, 13: 427-434.

 

Zhang, X., Yang, Z., Khan, S.I., Horton, J.R., Tamaru, H., Selker, E.U. and X. Cheng  (2003) Structural Basis for the Product Specificity of Histone Lysine Methyltransferases Mol. Cell 12: 177-185.

 

Selker, E.U., Tountas, N.A., Cross, S., Margolin, B.S., Murphy, J.G., Bird, A.P. and M Freitag.  2003) The methylated component of the Neurospora crassa genome, Nature 422: 893-897.

 

Galagan, J.E., Calvo, S.E., Borkovich, B.A., Selker, E.U., Read, N.D., et al. The genome sequence of the filamentous fungus Neurospora crassa (2003) Nature 422: 859-868.

 

Tamaru, H. Xing Zhang, X., McMillen, D., Singh, P.B., Nakayama, J., Grewal, S., Allis, C.D., Cheng, X. and E.U. Selker (2003) Trimethyl-Lysine9 of histone H3 is a mark for DNA methylation in Neurospora, Nature Genetics 34: 75-79.

 

Tamaru, H. and E. U. Selker (2003). Synthesis of Signals for de novo DNA Methylation in Neurospora crassa. Mol. Cell Biol. 23: 2379-2394.

 

Cheng, J.C., Matsen, C.B., Gonzales, F.A., Greer, S., Marquez, V.E., Jones, P.A., and E. U. Selker (2003)  Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst. 95:399-409.

 

Zhang, X., Tamaru, H., Khan, S.I., Horton, J.R., Keefe, L.J., Selker, E.U., and X. Cheng (2002). Structure of the Neurospora SET Domain Protein DIM-5, a Histone H3 Lysine Methyltransferase. Cell 111: 117-127.

 

Selker, E.U., Freitag, M., Kothe, G.O., Margolin, B.S., Rountree, M.R., Allis, C.D., and Tamaru, H. (2002). Induction and Maintenance of Non-Symmetrical DNA Methylation in Neurospora. Proc. Natl. Acad. Sci. USA 99: 16485–16490.

 

Freitag, M., Williams, R.L, Kothe, G.O., and E.U. Selker (2002). A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa  Proc. Natl. Acad. Sci. USA 99: 8802-8807.

 

Tamaru, H. and E.U. Selker (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa Nature 414: 277-283.

 

Kouzminova, E.A. and E.U. Selker (2001) Dim-2 encodes a DNA- methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO. J. 20: 4309-4323.

 

Miao, V. P. W., Freitag, M. and E.U. Selker (2000) Short TpA-rich segments of the ζ−η region induce DNA methylation in Neurospora crassa J. Mol. Biol. 300: 249-273.

 

Selker, E.U. (1998) Trichostatin A causes selective loss of DNA methylation in Neurospora.  Proc. Natl. Acad. Sci. USA 95: 9430-9435.

 

Rountree, M.R. and E.U. Selker (1997) DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes and Development 11: 2383-2395.

 

Cogoni, C., Irelan, J.T., Schumacher, M., Schmidhauser, T., Selker, E.U. 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: 3153-3163.

 

Cambareri, E.B., Foss, H.M., Rountree, M.R., Selker, E.U. and J A. Kinsey (1996) Epigenetic regulation of a transposon-inactivated gene in Neurospora is dependent on DNA methylation. Genetics 143: 137-146.

 

Singer, M.J., Marcotte, B.A. and E.U. Selker (1995) DNA methylation associated with repeat-induced point mutation (RIP) in Neurospora crassa. Mol. Cell. Biol. 15: 5586-5597.

 

Foss, H.M., Roberts, C.J., Claeys, K.M. and E.U. Selker (1993) Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation. Science 262: 1737-1741; correction: 267, 316.

 

Selker, E.U., Fritz, D.Y. and M.J. Singer (1993) Dense non-symmetrical DNA methylation resulting from repeat-induced point mutation (RIP) in Neurospora. Science 262: 1724-1728.

 

Cambareri, E.B., Singer, M.J. and E.U. Selker  (1991) Recurrence of repeat-induced point mutation (RIP) in Neurospora crassa. Genetics 127: 699-710.

 

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

 

Selker, E.U. (1990) DNA methylation and chromatin structure: a view from below. TIBS 15: 103-107.

 

Cambareri, E.B., Jensen, B.C., Schabtach, E. and E.U. Selker (1989) Repeat-induced G-C to A-T mutations in Neurospora. Science 244: 1571-1575.

 

Selker, E.U. and P.W. Garrett (1988) DNA sequence duplications trigger gene inactivation in Neurospora crassa. Proc. Natl. Acad. Sci. USA 85: 6870-6874.

 

Selker, E.U., Cambareri, E.B., Jensen, B.C. and K.R. Haack (1987) Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell 51: 741-752.

 

Selker, E.U., Jensen, B.C., and G.A. Richardson (1987) A portable signal causing faithful DNA methylation de novo in Neurospora crassa. Science 238: 48-53.

 

Selker, E.U., Morzycka-Wroblewska, E., Stevens, J.N. and R.L. Metzenberg (1986) An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes. Mol. Gen. Genet. 205: 189-192.

 

Selker, E.U. and J.N. Stevens (1985) DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc. Natl. Acad. Sci. USA 82: 8114-8118.

 

Selker, E.U., Stevens, J.N. and R.L. Metzenberg (1985) Heterogeneous 5S RNA in fungal ribosomes. Science 227: 1340-1343.

 

Selker, E.U., Yanofsky, C., Driftmier, K., Metzenberg, R.L., Alzner-DeWeerd, B. and U.L. RajBhandary (1981) Dispersed 5S RNA genes in N. crassa: Structure, expression and evolution. Cell 24: 819-828.