Abstract
BackgroundEukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt–Ada–Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question.Results Here we find that the SAGA/TREX-2 subunit Sus1 associates with upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitment to SAGA-dominated genes and RP genes is significantly disturbed under heat shock, with Sus1 relocated to environmental stress-responsive genes in these conditions. Moreover, in contrast to recent results showing that SAGA deubiquitinating enzyme Ubp8 is dispensable for RNA synthesis, genomic run-on experiments demonstrate that Sus1 contributes to synthesis and stability of a wide range of transcripts.ConclusionsOur study provides support for a model in which SAGA/TREX-2 factor Sus1 acts as a global transcriptional regulator in yeast but has differential activity at yeast genes as a function of their transcription rate or during stress conditions.
Highlights
Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt–Ada–Gcn5 acetyltransferase (SAGA)
The signal of an isogenic strain bearing no-tagged Sus1 was monitored (No-tag). b Gene-averaged 5′-ends of shifted relative read counts of Sus1-WT at 25 °C and at 37 °C around the transcription start site (TSS) in three gene classes: ribosomal pro‐ tein (RP) genes, SAGA-dominated genes and TFIID-dominated genes, with TSS oriented to the right
Note that ordinate scales vary for the three gene classes due to differences in the number of genes in each class. c) Signal tracks, showing unshifted ChIP-exo tag 5′-end reads for Sus1-wt at 25 °C and 37 °C at ribosomal protein (RP)-dependent gene RPL11, at SAGA-dependent gene CDC19 and at a TFIID-dominated gene SPB1 are shown
Summary
Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt–Ada–Gcn acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of most transcripts and are recruited genome-wide in yeast. How this broad recruitment confers selectivity under specific conditions remains an open question. While transcription of all genes requires the loading of the TATA-binding protein (TBP) onto their promoter sequences, differences exist in the co-regulators that are used. TATA-like containing genes are mainly dependent on the general transcription factor IID (TFIID), while the SAGA coactivator (Spt–Ada–Gcn acetyltransferase) plays a relatively greater role in the expression of TATA-box genes [2, 3]. The subunit composition is identical to that of SAGA, except that in SLIK the Spt subunit is C-terminally truncated by proteolytic cleavage, leading to release of the Spt subunit
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