Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing

Irvine, D. V., Goto, D. B., Vaughn, M. W., Nakaseko, Y., McCombie, W. R., Yanagida, M., Martienssen, R. (2009) Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome research, 19 (6). pp. 1077-83. ISSN 1088-9051 (Print)1088-9051 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/19423874
DOI: 10.1101/gr.089318.108

Abstract

Fission yeast is an important model for epigenetic studies due to the ease with which genetic mutants can be isolated. However, it can be difficult to complement epigenetic phenotypes with genomic libraries in order to identify the genes responsible. This is because epigenetic phenotypes are typically unstable, and can prohibit complementation if silencing cannot be reestablished. Here we have resequenced the fission yeast genome following mutagenesis to readily identify a novel mutant involved in heterochromatic silencing. Candidate genes were identified as functional single base changes linked to the mutation, which were then reconstituted in a wild-type strain to recapitulate the mutant phenotype. By this procedure we identified a weak allele of ubc4, which encodes an essential E2 ubiquitin ligase, as responsible for the swi*603 mutant phenotype. In combination with a large collection of mutants and suppressor plasmids, next-generation genomic resequencing promises to dramatically enhance the power of yeast genetics, permitting the isolation of subtle alleles of essential genes, alleles with quantitative effects, and enhancers and suppressors of heterochromatic silencing.

Item Type: Paper
Uncontrolled Keywords: Amino Acid Substitution Chromosome Mapping methods Chromosomes Fungal genetics Epigenesis Genetic Fungal Proteins genetics Genes Essential Genome Fungal genetics Mutation Phenotype Polymorphism Single Nucleotide Schizosaccharomyces genetics Sequence Analysis DNA methods Ubiquitin-Conjugating Enzymes genetics
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
Investigative techniques and equipment > assays
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > epigenetics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > epigenetics

Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 20 Feb 2013 19:43
Last Modified: 20 Feb 2013 19:43
PMCID: PMC2694473
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27409

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