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Gene. 2013 Aug 15;526(1):7-15. doi: 10.1016/j.gene.2013.05.016. Epub 2013 May 23.

Silencing near tRNA genes is nucleosome-mediated and distinct from boundary element function.

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Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109-0600, USA.


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.


ATPase; Ac; C terminus; CK2; Deacetylase; FOA; H2A; H2A.Z; H2B; H3; H4; Histone; Me; ORF; P; Phosphatase; RNA polymerase II; RNA polymerase III; RNA polymerase III transcription factor IIIB; RNA polymerase III transcription factor IIIC; RSC; Remodeling; Rpd3L; Rpd3S; SD; SGR; SHIMA; SINE; TFIIIB; TFIIIC; TOR; Target of Rapamycin; acetylation; carboxy terminus; casein kinase 2; chromatin remodeling complex; enzyme hydrolyzing adenosine triphosphate; fluoroorotic acid; histone H2A; histone H2B; histone H3; histone H4; histone variant H2A.Z; methylation; open reading frame; phosphorylation; pol II; pol III; protein complex containing Rpd3 protein; scanning histone mutagenesis with alanine; short interspersed element; synthetic yeast media with dextrose; synthetic yeast media with galactose and raffinose; tRNA; tRNA gene-mediated; tgm; tgm silencing; transfer RNA; ura; uracil

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