PMID:23707796

Citation	Good, PD, Kendall, A, Ignatz-Hoover, J, Miller, EL, Pai, DA, Rivera, SR, Carrick, B and Engelke, DR (2013) Silencing near tRNA genes is nucleosome-mediated and distinct from boundary element function. Gene 526:7-15
Abstract	Transfer RNA (tRNA) genes and other RNA polymerase III transcription units are dispersed in high copy throughout nuclear genomes, and can antagonize RNA polymerase II transcription in their immediate chromosomal locus. Previous work in Saccharomyces cerevisiae found that this local silencing required subnuclear clustering of the tRNA genes near the nucleolus. Here we show that the silencing also requires nucleosome participation, though the nature of the nucleosome interaction appears distinct from other forms of transcriptional silencing. Analysis of an extensive library of histone amino acid substitutions finds a large number of residues that affect the silencing, both in the histone N-terminal tails and on the nucleosome disk surface. The residues on the disk surfaces involved are largely distinct from those affecting other regulatory phenomena. Consistent with the large number of histone residues affecting tgm silencing, survey of chromatin modification mutations shows that several enzymes known to affect nucleosome modification and positioning are also required. The enzymes include an Rpd3 deacetylase complex, Hos1 deacetylase, Glc7 phosphatase, and the RSC nucleosome remodeling activity, but not multiple other activities required for other silencing forms or boundary element function at tRNA gene loci. Models for communication between the tRNA gene transcription complexes and local chromatin are discussed.
Links	PubMed PMC3745993 Online version:10.1016/j.gene.2013.05.016
Keywords	Amino Acid Sequence; Amino Acid Substitution; Chromatin Assembly and Disassembly/genetics; Gene Silencing; Genes, Fungal; Histones/chemistry; Histones/genetics; Histones/metabolism; Insulator Elements; Models, Molecular; Molecular Sequence Data; Mutation; Nucleosomes/genetics; Nucleosomes/metabolism; Protein Conformation; RNA Polymerase III/metabolism; RNA, Fungal/genetics; RNA, Fungal/metabolism; RNA, Transfer/genetics; RNA, Transfer/metabolism; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae/metabolism; Saccharomyces cerevisiae Proteins/chemistry; Saccharomyces cerevisiae Proteins/genetics; Saccharomyces cerevisiae Proteins/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
YEAST:RPD3	involved_in	GO:0061587: transfer RNA gene-mediated silencing	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
YEAST:PP12	involved_in	GO:0061587: transfer RNA gene-mediated silencing	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete

References

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