The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

Abstract

Saccharomyces cerevisiae telomeres have been a paradigm for studying telomere position effects on gene expression. Telomere position effect was first described in yeast by its effect on the expression of reporter genes inserted adjacent to truncated telomeres. The reporter genes showed variable silencing that depended on the Sir2/3/4 complex. Later studies examining subtelomeric reporter genes inserted at natural telomeres hinted that telomere position effects were less pervasive than previously thought. Additionally, more recent data using the sensitive technology of chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) revealed a discrete and noncontinuous pattern of coenrichment for all three Sir proteins at a few telomeres, calling the generality of these conclusions into question. Here we combined the ChIP-Seq of the Sir proteins with RNA sequencing (RNA-Seq) of messenger RNAs (mRNAs) in wild-type and in SIR2, SIR3, and SIR4 deletion mutants to characterize the chromatin and transcriptional landscape of all native S. cerevisiae telomeres at the highest achievable resolution. Most S. cerevisiae chromosomes had subtelomeric genes that were expressed, with only 6% of subtelomeric genes silenced in a SIR-dependent manner. In addition, we uncovered 29 genes with previously unknown cell-type-specific patterns of expression. These detailed data provided a comprehensive assessment of the chromatin and transcriptional landscape of the subtelomeric domains of a eukaryotic genome.KEYWORDS Sir complex; telomeres; ChIP-Seq; RNA-Seq; mating-type regulation T ELOMERES are specialized structures at the ends of eukaryotic chromosomes that are critical for various biological functions. Telomeres bypass the problem of replicating the ends of linear DNA, protect chromosome ends from exonucleases and nonhomologous end joining, prevent the linear DNA ends from activating a DNA-damage checkpoint, and exhibit suppressed recombination [reviewed in Wellinger and Zakian (2012)]. In Saccharomyces cerevisiae, telomeres are composed of three sequence features: telomeric repeats, which consist of 300 6 75 bp of (TG 1-3 ) n repeated units produced by telomerase; X elements; and Y9 elements, which contain an ORF for a putative helicase gene. The X elements are subdivided into a core X [consisting of an autonomously replicating sequence (ARS) consensus sequence and an Abf1-binding site] and subtelomeric repeats that have variable numbers of repeated units containing a binding site for Tbf1 (Louis 1995). All telomeres contain telomeric repeats plus an X element, and about half of S. cerevisiae's 32 telomeres also contain a Y9 element (X-Y9 telomeres). X-only telomeres contain an X element but not a Y9 element. Unlike the Y9 elements, the telomeric repeats and X elements are bound by proteins that are critical for maintenance of telomeres. Rap1 binds the TG 1-3 telomeric repeats and recruits the Sir2/3/4 protein complex, the trio of heterochromatin structural proteins critical for repression of the silent mating ...

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

“…These proto-silencers include ORC binding sites within repetitive subtelomeric X elements (Figure 3). Unexpectedly, Ume6 binding sites in the promoters of some subtelomeric seripauperin genes (PAU genes) also act as proto-silencers (RadmanLivaja et al 2011;Ellahi et al 2015).…”

“…Sir3 and Sir4 associate with Rap1 and Sir4 associates with ORC-bound Sir1 (Moretti et al 1994;Triolo and Sternglanz 1996;Moretti and Shore 2001;Chen et al 2011). In catalytic mutants of Sir2, the Sir2/3/4 complex is restricted to silencers (Hoppe et al 2002;Rusche et al 2002;Ellahi et al 2015). Thus, the action of Sir2 on histone substrates triggers the transition from nucleation to spreading.…”

“…At the HM loci, silent chromatin spans several kilobases and represses pairs of genes, the a genes at HMR and the a genes at HML, required for haploid mating-type identity. At telomeric sites, the size of the domains varies substantially from one telomere to the next with many telomeres possessing only small and often discontinuous silent chromatin domains (Fourel et al 1999;Pryde and Louis 1999;Takahashi et al 2011;Ellahi et al 2015). Only a fraction of subtelomeric genes are subject to transcriptional silencing by the Sir proteins.…”

Nutritional Control of Chronological Aging and Heterochromatin inSaccharomyces cerevisiae

“…Interestingly, subtelomeric regions are enriched for genes with a role in metabolism (Ai et al 2002), although few subtelomeric genes significantly increase in expression over wild-type levels in a sir2D strain during log-phase growth in 2% glucose (Ellahi et al 2015). However, it is possible that expression levels of important metabolic genes do change in a Sir2-dependent manner at higher glucose concentrations and/or during stationary phase.…”

Functions for diverse metabolic activities in heterochromatin

“…Silencing at telomeres and the HM loci was long considered to follow a sequential model: initial deacetylation by Sir2 creates binding sites for Sir3 and Sir4, which in turn regulate the spreading of Sir2 across these regions (5). More recent high-resolution studies report a less uniform landscape for silenced chromatin (6), although the central importance of the Sir proteins remains clear. They, together with transcription factors including Rap1 and Abf1, form a multisubunit silencing complex known as the silent information regulator (SIR) complex.…”