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

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.

Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis

“…Some active tRNA genes have been shown to possess chromatin insulator activity (35,81,82). In addition, extensive work in yeast has demonstrated that active tRNA genes can repress neighboring Pol II genes through tgm silencing (34,83,84). To understand whether AGO2 plays a role in either of these processes, we focused on a region on the p arm of human chromosome 17 that has been previously characterized to have active tRNA genes that can act as insulators (35).…”

“…The increase in gene expression (FPKM) among genes that flank AGO2-bound tRNA genes upon AGO2 knockdown suggested a cis effect exerted by the actively transcribed tRNA gene upon nearby Pol II genes, similar to tgm silencing in yeast (34,83,84). To address this possibility, we quantified the fold change in each upstream and downstream Pol II gene as a function of its distance from the nearest tRNA gene (Fig.…”

The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer

“…The involvement of nucleosome surfaces and several chromatin modifying and remodeling enzymes in tgm silencing has been documented, though how the tRNA gene communicates physically with the chromatin is not yet understood (Good et al, 2013). Mutations affecting nucleosome covalent modification and remodeling include those in the RSC nucleosome remodeling complex subunits, Rpd3 deacetylase subunits, Hos1 deacetylase, and the Glc7 phosphatase (Good et al, 2013).…”

“…The involvement of nucleosome surfaces and several chromatin modifying and remodeling enzymes in tgm silencing has been documented, though how the tRNA gene communicates physically with the chromatin is not yet understood (Good et al, 2013). Mutations affecting nucleosome covalent modification and remodeling include those in the RSC nucleosome remodeling complex subunits, Rpd3 deacetylase subunits, Hos1 deacetylase, and the Glc7 phosphatase (Good et al, 2013). Taken together with the association of Mod5 with pre-tRNAs and the transcription complexes, we propose that the Mod5-pre-tRNA complex might help recruit one or more of the chromatin-modifying enzymes that exert a repressive effect on nearby promoters through nucleosome rearrangement.…”

Ty3, a Position-specific Retrotransposon in Budding Yeast

“…Ty3 could use identical genes at widely differing frequencies because of different chromatin contexts. RNAP III genes undergo specific types of epigenetic modifications and bind chromatin remodelers and condensins (179)(180)(181)(182)(183)(184)(185)(186)(187)(188)(189)(190). In addition to possible differences in chromatin context, tDNAs also act as replication fork barriers (191), and subpopulations localize to the nucleolus (31,192) and nuclear pores (30).…”