Dynamic reprogramming of transcription factors to and from the subtelomere

Abstract

Transcription factors are most commonly thought of as proteins that regulate expression of specific genes, independently of the order of those genes along the chromosome. By screening genome-wide chromatin immunoprecipitation (ChIP) profiles in yeast, we find that more than 10% of DNA-binding transcription factors concentrate at the subtelomeric regions near to chromosome ends. None of the proteins identified were previously implicated in regulation at telomeres, yet genomic and proteomic studies reveal that a subset of factors show many interactions with established telomere binding complexes. For many factors, the subtelomeric binding pattern is dynamic and undergoes flux toward or away from the telomere as physiological conditions shift. We find that subtelomeric binding is dependent on environmental conditions and correlates with the induction of gene expression in response to stress. Taken together, these results underscore the importance of genome structure in understanding the regulatory dynamics of transcriptional networks.

Environment‐responsive transcription factors bind subtelomeric elements and regulate gene silencing

“…In particular, Oaf1p binds X elements and enhances this silencing in response to fatty acid exposure, and Rox1p, Gzf3p and Phd1p bind and conditionally antagonize silencing in response to exposure to H 2 O 2 , rapamycin and butanol, respectively (Figure 5 and Supplementary Figure S4). Analysis of conditional Oaf1p‐mediated silencing showed that it is dependent on SIR2 but not HDA1 , consistent with a novel role for TFs in X element‐mediated silencing that is distinct from their roles related to Hda1p at other subtelomeric loci (Mak et al , 2009).…”

Mapping Yeast Transcriptional Networks

“…The promoters that are generally occupied by a larger number of TFs tend to correspond to genes located near autonomously replicating sequences, Ty1 transposons, centromeres, and subtelomeric regions. Indeed, two recent reanalyses of these data found that >10% of TFs bind in subtelomeric regions (Mak et al 2009; Smith et al 2011); the latter study also observed a similar trend for other TFs (Smith et al 2011). A similar phenomenon was reported for Caenorhabditis elegans and Drosophila , with certain regions being highly bound by many different transcription factors [so-called highly occupied target (“HOT”) regions] (Moorman et al 2006; Gerstein et al 2010; Roy et al 2010).…”

Interplay among Gcn5, Sch9 and Mitochondria during Chronological Aging of Wine Yeast Is Dependent on Growth Conditions

“…Given the important role of Sch9 in CLS, we searched the Saccharomyces Genome Database (SGD) to find the physical and genetic connections between Gcn5 and Sch9. Sch9 interacts physically and genetically to transcription factor Rgm1 [ 34 ], which has been linked to subtellomeric binding [ 35 ]. RGM1 also interacts genetically to GCN5 [ 36 ], so we further investigated the role and interaction of this gene in aging.…”