Architectural Mediator subunits are differentially essential for global transcription in <i>Saccharomyces cerevisiae</i>

Tourigny, Jason P; Schumacher, Kenny; Saleh, Moustafa M.; Devys, Didier; Zentner, Gabriel E.

doi:10.1093/genetics/iyaa042

Cited by 14 publications

(13 citation statements)

References 67 publications

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“…To explore this further, we compared the genome distribution of non-RPG SUMO peaks with the distribution of a GTF component, TFIIF, as determined by analysis of a previously reported Tfg2 ChIP-seq dataset [ 49 ]. If SUMO peaks at promoters of non-RPGs derive from sumoylated GTFs, then we might expect SUMO to be more readily detected on genes that have high levels of GTF components.…”

Section: Resultsmentioning

confidence: 99%

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II

et al. 2021

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Transcription-related proteins are frequently identified as targets of sumoylation, including multiple subunits of the RNA polymerase II (RNAPII) general transcription factors (GTFs). However, it is not known how sumoylation affects GTFs or whether they are sumoylated when they assemble at promoters to facilitate RNAPII recruitment and transcription initiation. To explore how sumoylation can regulate transcription genome-wide, we performed SUMO ChIP-seq in yeast and found, in agreement with others, that most chromatin-associated sumoylated proteins are detected at genes encoding tRNAs and ribosomal proteins (RPGs). However, we also detected 147 robust SUMO peaks at promoters of non-ribosomal protein-coding genes (non-RPGs), indicating that sumoylation also regulates this gene class. Importantly, SUMO peaks at non-RPGs align specifically with binding sites of GTFs, but not other promoter-associated proteins, indicating that it is GTFs specifically that are sumoylated there. Predominantly, non-RPGs with SUMO peaks are among the most highly transcribed, have high levels of TFIIF, and show reduced RNAPII levels when cellular sumoylation is impaired, linking sumoylation with elevated transcription. However, detection of promoter-associated SUMO by ChIP might be limited to sites with high levels of substrate GTFs, and promoter-associated sumoylation at non-RPGs may actually be far more widespread than we detected. Among GTFs, we found that TFIIF is a major target of sumoylation, specifically at lysines 60/61 of its Tfg1 subunit, and elevating Tfg1 sumoylation resulted in decreased interaction of TFIIF with RNAPII. Interestingly, both reducing promoter-associated sumoylation, in a sumoylation-deficient Tfg1-K60/61R mutant strain, and elevating promoter-associated SUMO levels, by constitutively tethering SUMO to Tfg1, resulted in reduced RNAPII occupancy at non-RPGs. This implies that dynamic GTF sumoylation at non-RPG promoters, not simply the presence or absence of SUMO, is important for maintaining elevated transcription. Together, our findings reveal a novel mechanism of regulating the basal transcription machinery through sumoylation of promoter-bound GTFs.

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Section: Resultsmentioning

confidence: 99%

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II

et al. 2021

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“…The head and middle modules, in conjunction with the scaffold subunit Med14, form core Mediator (cMed), which is sufficient for Mediator function in vitro [2,3]. Accordingly, depletion of Med14 results in a marked global decrease of RNAPII occupancy [4] and nascent transcription [5]. Similarly, disruption of the head module via a temperature-sensitive Med17 mutation or Med17 depletion drastically reduces nascent RNA synthesis across most RNAPII-dependent genes [2,5].…”

Section: Introductionmentioning

confidence: 99%

“…Accordingly, depletion of Med14 results in a marked global decrease of RNAPII occupancy [4] and nascent transcription [5]. Similarly, disruption of the head module via a temperature-sensitive Med17 mutation or Med17 depletion drastically reduces nascent RNA synthesis across most RNAPII-dependent genes [2,5].…”

Section: Introductionmentioning

confidence: 99%

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters

et al. 2021

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The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We propose that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters

Saleh

Jeronimo

Robert

et al. 2021

Preprint

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The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

show abstract

Architectural Mediator subunits are differentially essential for global transcription in Saccharomyces cerevisiae

Cited by 14 publications

References 67 publications

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II

Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters

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