Genome-wide analysis of functional sirtuin chromatin targets in yeast

Abstract

BackgroundThe sirtuins are a conserved family of NAD+-dependent histone/protein deacetylases that regulate numerous cellular processes, including heterochromatin formation and transcription. Multiple sirtuins are encoded by each eukaryotic genome, raising the possibility of cooperativity or functional overlap. The scope and variety of chromatin binding sites of the sirtuins in any specific organism remain unclear.ResultsHere we utilize the ChIP-seq technique to identify and functionally characterize the genome-wide targets of the sirtuins, Sir2, Hst1 to Hst4, and the DNA binding partner of Hst1, Sum 1, in Saccharomyces cerevisiae. Unexpectedly, Sir2, Hst1 and Sum1, but not the other sirtuins, exhibit co-enrichment at several classes of chromatin targets. These include telomeric repeat clusters, tRNA genes, and surprisingly, the open reading frames (ORFs) of multiple highly expressed RNA polymerase II-transcribed genes that function in processes such as fermentation, glycolysis, and translation. Repression of these target genes during the diauxic shift is specifically dependent on Sir2/Hst1/Sum1 binding to the ORF and sufficiently high intracellular NAD+ concentrations. Sir2 recruitment to the ORFs is independent of the canonical SIR complex and surprisingly requires Sum1. The shared Sir2/Hst1/Sum1 targets also significantly overlap with condensin and cohesin binding sites, where Sir2, Hst1, and Sum1 were found to be important for condensin and cohesin deposition, suggesting a possible mechanistic link between metabolism and chromatin architecture during the diauxic shift.ConclusionsThis study demonstrates the existence of overlap in sirtuin function, and advances our understanding of conserved sirtuin-regulated functions, including the regulation of glycolytic gene expression and condensin loading.

Sirtuin A regulates secondary metabolite production by <i>Aspergillus nidulans</i>

“…These categories include genes for carbon source (glucose) and amino acid metabolism, indicating that SirA up-regulates the genes for the primary metabolism during the late stage of culture. This finding was in contrast to those derived from S. cerevisiae sirtuin Sir2p and Hst1p that repress the expression of genes for glycolysis, and, hence, shift metabolism upon exiting the exponential growth phase (Li et al, 2013), and agreed with findings of previous transcriptome analyses indicating that Table 3. Gene ontology terms enriched among regulated genes in SirAD.…”

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

“…Recruitment of RENT by Pol I at NTS2 is dynamic, as might be expected for a translocating enzyme. ChIP assays suggest that RENT tracks with the polymerase for a short distance after initiation, spreading into the 59 externally-transcribed spacer (59-ETS) region (Huang and Moazed 2003;Li et al 2013). Only 50% of the rDNA genes in a growing cell are transcribed by Pol I at a given time (Dammann et al 1993), so it is possible that RENT recruitment to NTS2 is restricted to activelytranscribed rDNA genes.…”

The Chromatin and Transcriptional Landscape of NativeSaccharomyces cerevisiaeTelomeres and Subtelomeric Domains

“…We also observed regions of H4K16 hypoacetylation without detectable Sir2 association, which presumably reflected the action of a different histone deacetylase such as Rpd3 or Hst1. Both have been shown to associate with subtelomeric chromatin (Kurdistani et al 2002;Ehrentraut et al 2010;Li et al 2013). Alternatively, the hyopacetylation of H4K16 in these regions could be due to transient Sir2 association not captured by ChIP-Seq.…”