Institute of Molecular Biology

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Eric U. Selker

Eric U. Selker

Professor, Biology
Member, IMB

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

Office: Streisinger Hall Room 355D
Office Phone: 541-346-5193
Lab: Streisinger Hall Room 355D
Lab Phone: 541-346-5197

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Research Interests

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.

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

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).

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

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

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

Group Members

Andy Klocko
Andy Klocko
S honda
Tereza Ormsby
Andy Klocko
Kevin McNaught
S honda
Jordan Gessaman
S honda
Vince Bicocca
Andy Klocko
Tish T. Wiles

Recent publications

(pulled from pubmed)

Recent publications

(pulled from pubmed)

The cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora crassa.
Adhvaryu KK, Gessaman JD, Honda S, Lewis ZA, Grisafi PL, Selker EU
Eukaryot Cell 2015 Jan;14(1):25-8
Neurospora importin ╬▒ is required for normal heterochromatic formation and DNA methylation.
Klocko AD, Rountree MR, Grisafi PL, Hays SM, Adhvaryu KK, Selker EU
PLoS Genet 2015 Mar;11(3):e1005083
Regional control of histone H3 lysine 27 methylation in Neurospora.
Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU
Proc Natl Acad Sci U S A 2013 Apr 9;110(15):6027-32
Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation.
Honda S, Lewis ZA, Shimada K, Fischle W, Sack R, Selker EU
Nat Struct Mol Biol 2012 Apr 15;19(5):471-7, S1
Selker EU
Curr Biol 2011 Feb 22;21(4):R139-40
Substitutions in the amino-terminal tail of neurospora histone H3 have varied effects on DNA methylation.
Adhvaryu KK, Berge E, Tamaru H, Freitag M, Selker EU
PLoS Genet 2011 Dec;7(12):e1002423
PARP is involved in replicative aging in Neurospora crassa.
Kothe GO, Kitamura M, Masutani M, Selker EU, Inoue H
Fungal Genet Biol 2010 Apr;47(4):297-309
The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassa.
Honda S, Lewis ZA, Huarte M, Cho LY, David LL, Shi Y, Selker EU
Genes Dev 2010 Mar 1;24(5):443-54
Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatin.
Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Selker EU
Proc Natl Acad Sci U S A 2010 May 4;107(18):8310-5
DNA methylation and the formation of heterochromatin in Neurospora crassa.
Rountree MR, Selker EU
Heredity (Edinb) 2010 Jul;105(1):38-44
Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa.
Anderson DC, Green GR, Smith K, Selker EU
Biochemistry 2010 Jun 29;49(25):5244-57
H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa.
Smith KM, Dobosy JR, Reifsnyder JE, Rountree MR, Anderson DC, Green GR, Selker EU
Genetics 2010 Dec;186(4):1207-16
DNA methylation and normal chromosome behavior in Neurospora depend on five components of a histone methyltransferase complex, DCDC.
Lewis ZA, Adhvaryu KK, Honda S, Shiver AL, Knip M, Sack R, Selker EU
PLoS Genet 2010 Nov 4;6(11):e1001196
Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa.
Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Sch├╝beler D, Selker EU
Genome Res 2009 Mar;19(3):427-37
Characterization of chromosome ends in the filamentous fungus Neurospora crassa.
Wu C, Kim YS, Smith KM, Li W, Hood HM, Staben C, Selker EU, Sachs MS, Farman ML
Genetics 2009 Mar;181(3):1129-45
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA
PLoS One 2008;3(10):e3376
The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9.
Smith KM, Kothe GO, Matsen CB, Khlafallah TK, Adhvaryu KK, Hemphill M, Freitag M, Motamedi MR, Selker EU
Epigenetics Chromatin 2008 Nov 3;1(1):5
Protein phosphatase PP1 is required for normal DNA methylation in Neurospora.
Adhvaryu KK, Selker EU
Genes Dev 2008 Dec 15;22(24):3391-6
High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora.
Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU
Genetics 2007 Oct;177(2):1163-71
Controlling DNA methylation: many roads to one modification.
Freitag M, Selker EU
Curr Opin Genet Dev 2005 Apr;15(2):191-9
Methylation of histone H3 lysine 36 is required for normal development in Neurospora crassa.
Adhvaryu KK, Morris SA, Strahl BD, Selker EU
Eukaryot Cell 2005 Aug;4(8):1455-64
HP1 is essential for DNA methylation in neurospora.
Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU
Mol Cell 2004 Feb 13;13(3):427-34
DNA methylation is independent of RNA interference in Neurospora.
Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R, Selker EU
Science 2004 Jun 25;304(5679):1939
GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa.
Freitag M, Hickey PC, Raju NB, Selker EU, Read ND
Fungal Genet Biol 2004 Oct;41(10):897-910
Genome defense and DNA methylation in Neurospora.
Selker EU
Cold Spring Harb Symp Quant Biol 2004;69:119-24
Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa.
Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU
Nat Genet 2003 May;34(1):75-9
The methylated component of the Neurospora crassa genome.
Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M
Nature 2003 Apr 24;422(6934):893-7