Abstract
Modifier of transcription 1 (Mot1) is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the facilitates chromatin transcription (FACT) histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we found that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5' ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation.
Highlights
Modifier of transcription 1 (Mot1)4 was originally identified genetically as a negative regulator of transcription from weak promoters [1,2,3,4,5,6,7]
Mot1 and Spt16 Co-Regulate Transcription—Here we report a functional overlap in transcriptional control between Mot1 and Spt16 that operates on a global scale with ϳ1,300 genes controlled by both factors
The physical and genetic interactions between Mot1 and Spt16 further suggest that these two factors function together in vivo
Summary
Mot and Spt Genetically and Physically Interact—Mot and Spt have been implicated in transcription initiation and elongation but through different mechanisms. Mutation of Mot by itself mainly affected the ϩ1 and ϩ2 nucleosomes regardless of gene expression outcome, comparison of spt197 with the double mutant reveals a more expansive co-regulatory role for Mot in gene repression with effects on nucleosome occupancy that extend at least several hundred base pairs in both directions from the TSS. Mot and Spt Affect the Position of the ϩ1 Nucleosome—In addition to affecting occupancy and fuzziness, it appeared from the gene average plots in Fig. 9 that loss of one or both of these factors shifted the median position of promoter-proximal nucleosomes with respect to the TSS Such an effect has been reported previously for Spt16 [65]. Nucleosomes at ϩ2 and ϩ3 positions showed significant position shifts in all three mutants as did ϩ4 and ϩ5 nucleosomes in spt197 cells, consistent with the loss of nucleosome organization in this mutant and the double mutant
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