Research Topics
| ERIC SELKERSummaryAffiliation: University of Oregon Country: USA Publications
Research Grants
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Detail Information
Publications
Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion?E U Selker
Institute of Molecular Biology, University of Oregon, Eugene 97403, USA
Trends Genet 13:296-301. 1997..Together, these processes should limit the proliferation of transposable elements and serve to preserve the overall structure of the genome...- Repeat-induced gene silencing in fungiEric U Selker
Institute of Molecular Biology, University of Oregon, Eugene 97403, USA
Adv Genet 46:439-50. 2002 
Induction and maintenance of nonsymmetrical DNA methylation in NeurosporaEric U Selker
Institute of Molecular Biology, University of Oregon, Eugene 97403 1229, USA
Proc Natl Acad Sci U S A 99:16485-90. 2002..DNA methylation indirectly recruits histone deacetylases, providing the framework of a self-reinforcing system that could result in propagation of DNA methylation and the associated silenced chromatin state...- The methylated component of the Neurospora crassa genomeEric U Selker
Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
Nature 422:893-7. 2003..DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation--a genome defence system that mutates duplicated sequences... - DNA methylation is independent of RNA interference in NeurosporaMichael Freitag
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
Science 304:1939. 2004 - Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassaZachary A Lewis
Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403 1229, USA
Genome Res 19:427-37. 2009..These data show that A:T-rich RIP'd DNA efficiently directs methylation of H3K9, which in turn, directs methylation of associated cytosines... - Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassaHisashi Tamaru
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
Nat Genet 34:75-9. 2003..crassa. Here we show that trimethylated H3 Lys9, but not dimethylated H3 Lys9, marks chromatin regions for cytosine methylation and that DIM-5 specifically creates this mark... - Synthesis of signals for de novo DNA methylation in Neurospora crassaHisashi Tamaru
Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
Mol Cell Biol 23:2379-94. 2003.... - Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassaShinji Honda
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 1229, USA
Mol Cell Biol 28:6044-55. 2008.... - Methylation of histone H3 lysine 36 is required for normal development in Neurospora crassaKeyur K Adhvaryu
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
Eukaryot Cell 4:1455-64. 2005..Taken together, our results suggest that methylation of K36 in Neurospora crassa is essential for normal growth and development... - Robert L. Metzenberg, June 11, 1930-July 15, 2007: geneticist extraordinaire and "model human"Eric U Selker
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
Genetics 178:611-9. 2008 - Controlling DNA methylation: many roads to one modificationMichael Freitag
Institute of Molecular Biology and Department of Biology, University of Oregon, Eugene, OR 97403, USA
Curr Opin Genet Dev 15:191-9. 2005..Despite recent progress, classic questions remain, including: What are the signals for DNA methylation? Are "de novo" and "maintenance" methylation truly separate processes? How is DNA methylation regulated?.. - GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassaMichael Freitag
Institute of Molecular Biology and Department of Biology, University of Oregon, Eugene, OR 97403, USA
Fungal Genet Biol 41:897-910. 2004..H1-GFP was translated in the vicinity of hH1+-sgfp+ nuclei in the common cytoplasm of giant Banana ascospores, but it diffused into all nuclei, another illustration of the utility of GFP fusion proteins... - The DMM complex prevents spreading of DNA methylation from transposons to nearby genes in Neurospora crassaShinji Honda
Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, 97403, USA
Genes Dev 24:443-54. 2010..DMM-1 relies on an associated protein, DMM-2, which bears a DNA-binding motif, for localization and proper function. HP1 is required to recruit the DMM complex to the edges of methylated regions... - HP1 is essential for DNA methylation in neurosporaMichael Freitag
Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403 USA
Mol Cell 13:427-34. 2004..Unlike mutants that lack DNA methyltransferase, mutants with defects in the HP1 gene hpo exhibit severe growth defects, suggesting that HP1 is required for processes besides DNA methylation... - High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in NeurosporaZachary A Lewis
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
Genetics 177:1163-71. 2007..crassa strains: Mauriceville and Oak Ridge. Furthermore, RAD mapping was used to quickly map a previously unknown gene, defective in methylation-7 (dim-7)... - Identification of DIM-7, a protein required to target the DIM-5 H3 methyltransferase to chromatinZachary A Lewis
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
Proc Natl Acad Sci U S A 107:8310-5. 2010..In addition, we found that DIM-7 is essential for recruitment of DIM-5 to form heterochromatin... - Protein phosphatase PP1 is required for normal DNA methylation in NeurosporaKeyur K Adhvaryu
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
Genes Dev 22:3391-6. 2008..Similarly, amino acid substitutions of H3S10 abolished methylation of H3K9 and DNA. Thus, H3S10 dephosphorylation by PP1 is required for DNA methylation of some loci... - Identification and characterization of the genes encoding the core histones and histone variants of Neurospora crassaShan M Hays
Department of Biology and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1229, USA
Genetics 160:961-73. 2002..This may be a reflection of the evolution of the RIP (repeat-induced point mutation) and MIP (methylation induced premeiotically) processes that detect sizable duplications and silence associated genes... - PARP is involved in replicative aging in Neurospora crassaGregory O Kothe
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States
Fungal Genet Biol 47:297-309. 2010..PARPs may regulate aging by impacting NAD+/NAM availability, thereby influencing Sirtuin activity, or they may function in alternative NAD+-dependent or NAD+-independent aging pathways... - Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purificationShinji Honda
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
Genetics 182:11-23. 2009..Features of the new vectors allowed for verification of an interaction between HP1 and DIM-2 in vivo by Co-IP assays on proteins expressed either from their native loci or from the his-3 locus... - A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassaMichael Freitag
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229, USA
Proc Natl Acad Sci U S A 99:8802-7. 2002..We isolated homologues of rid from Neurospora tetrasperma and Neurospora intermedia to identify conserved regions. Homologues possess all motifs characteristic of eukaryotic DMTs and have large distinctive C- and N-terminal domains... 
Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassaD C Anderson
Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
Biochemistry 49:5244-57. 2010..Combined with asymmetry-generated diversity in H2B structural states in nucleosome core particles, the extensive modifications identified here can create substantial histone-generated structural diversity in nucleosome core particles...- Rapid SNP discovery and genetic mapping using sequenced RAD markersNathan A Baird
Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
PLoS ONE 3:e3376. 2008..Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms... - Molecular biology. A self-help guide for a trim genomeEric U Selker
Science 300:1517-8. 2003 - RIP: the evolutionary cost of genome defenseJames E Galagan
Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 04124, USA
Trends Genet 20:417-23. 2004..Most if not all paralogs in N. crassa duplicated and diverged before the emergence of RIP. Thus, RIP illustrates the extraordinary extent to which genomes will go to defend themselves against mobile genetic elements... - The genome sequence of the filamentous fungus Neurospora crassaJames E Galagan
Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
Nature 422:859-68. 2003..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes... - In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferasesRobert E Collins
Biochemistry and Chemistry, Emory University, Atlanta, GA 30392, USA
J Biol Chem 280:5563-70. 2005..The altered DIM-5 rescued the growth defect characteristic of dim-5 N. crassa but did not fully rescue the gross DNA hypomethylation of dim-5 strains... - Structural basis for the product specificity of histone lysine methyltransferasesXing Zhang
Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
Mol Cell 12:177-85. 2003.... - Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferaseXing Zhang
Department of Biochemistry, School of Medicine, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
Cell 111:117-27. 2002..The structure suggests a mechanism for the methylation reaction and provides the structural basis for functional characterization of the HKMT family and the SET domain... - Inhibition of DNA methylation and reactivation of silenced genes by zebularineJonathan C Cheng
University of Southern California/Norris Comprehensive Cancer Center and Hospital, Department of Biochemistry and Molecular Biology, USC Keck School of Medicine, Los Angeles 90089, USA
J Natl Cancer Inst 95:399-409. 2003..001) or by oral gavage (P<.001). CONCLUSIONS: Zebularine is a stable DNA demethylating agent and the first drug in its class able to reactivate an epigenetically silenced gene by oral administration... - Histone H1 Is required for proper regulation of pyruvate decarboxylase gene expression in Neurospora crassaH Diego Folco
, , , , , Argentina
Eukaryot Cell 2:341-50. 2003..Thus, Neurospora histone H1 is required for the proper regulation of cfp, a gene with a key role in the respiratory-fermentative pathway... - Recurrent locus-specific mutation resulting from a cryptic ectopic insertion in NeurosporaDavid D Perkins
Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
Genetics 175:527-44. 2007..These findings support a model in which an ectopic insertion that created a mutation at the target site acts as a locus-specific mutator via RIP... - The Neurospora crassa White Collar-1 dependent blue light response requires acetylation of histone H3 lysine 14 by NGF-1Benedetto Grimaldi
Dipartimento di Genetica e Biologia Molecolare, , 00185 Rome, Italy
Mol Biol Cell 17:4576-83. 2006..Together, our findings reveal a direct link between histone modification and light signaling in Neurospora and contribute to the developing understanding of the molecular mechanisms operating in light-inducible gene activation... - A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulansDong W Lee
Department of Biology, College of Science, Texas A and M University, College Station, Texas, United States of America
PLoS ONE 3:e2531. 2008..We discovered a close homologue in Aspergillus nidulans, a fungus thought to have no methylation and no genome defense system comparable to RIP or MIP... - The 2005 Thomas Hunt Morgan Medal. Robert L. MetzenbergEric U Selker
Genetics 169:503-5. 2005 - Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzaeJames E Galagan
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
Nature 438:1105-15. 2005..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation... - Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organismKatherine A Borkovich
Department of Plant Pathology, University of California, Riverside, California 92521, USA
Microbiol Mol Biol Rev 68:1-108. 2004..The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease... - A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genesRichard J Roberts
New England Biolabs, Beverly, MA 01915, USA
Nucleic Acids Res 31:1805-12. 2003..It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes...
Research Grants
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 1993..Mutants defective in other genes necessary for methylation will be isolated using two approaches - one using a selection successful in a preliminary experiment, and the other using "brute force" to obtain all possible mutants...
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 2002..Methylation mutants and methods that we have developed to study replication in Neurospora will be used to investigate whether either DNA methylation or histone hypoacetylation cause late replication of DNA. ..
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 2007..To test the possible role of chromatin remodeling in DNA methylation; 7. To identify additional components of the DNA methvlation machinerv. ..
- GENETIC ASPECTS OF DNA METHYLATIONERIC SELKER; Fiscal Year: 1990