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Kin28 regulates the transient association of Mediator with core promoters

Nature Structural & Molecular Biology volume 21, pages 449–455 (2014)Cite this article

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Abstract

Mediator is an essential, broadly used eukaryotic transcriptional coactivator. How and what Mediator communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence, upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity or in cells in which the RNAPII C-terminal domain is mutated to replace Ser5 with alanine, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is released quickly from promoters after phosphorylation of Ser5 by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter.

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Figure 1: Mediator occupies the UAS.
Figure 2: Mediator is involved in PIC assembly in vivo.
Figure 3: Mediator accumulates at core promoters in the absence of Kin28 kinase activity (Supplementary Fig. 3).
Figure 4: The CAND system to study CTD function in vivo.
Figure 5: Mediator occupancy shifts toward core promoters in the absence of CTD Ser5 phosphorylation.
Figure 6: A schematic representation of the dynamic association of Mediator with yeast genes.

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Acknowledgements

We thank K. Struhl (Harvard Medical School) for discussing unpublished data and P. Collin (Robert laboratory) for assistance with the CTD mutant constructs, as well as R. Young (Whitehead Institute for Biomedical Research), S. Hahn (Fred Hutchinson Cancer Research Center) and L. Myers (Dartmouth-Hitchcock Medical Center) for sharing strains and antibodies. We are also grateful to C. Kaplan and N. Francis for their critical reading of the manuscript. This work was funded by a Canadian Institutes of Health Research grant (MOP-82891) to F.R.

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Authors and Affiliations

  1. Institut de recherches cliniques de Montréal, Montréal, Québec, Canada

    Célia Jeronimo & François Robert

  2. Département de Médecine, Université de Montréal, Montréal, Québec, Canada

    François Robert

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  1. Célia Jeronimo
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C.J. and F.R. designed the project and wrote the manuscript. C.J. performed most of the experiments. F.R. performed most of the analyses.

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Correspondence to François Robert.

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Integrated supplementary information

Supplementary Figure 1 Enrichment in highly transcribed coding regions is often observed in ChIP experiments and has to be controlled for.

(a) Enrichment of various Mediator subunits at the highly transcribed PMA1 gene as determined by ChIP-chip using a panel of rabbit polyclonal antibodies (green), as well as using a control IgG antibody (black). All ChIPs were hybridized (and therefore normalized) against input DNA. (b) A scatter plot of the enrichment over coding regions in a control IgG ChIP and an Rpb3 ChIP. (c) Enrichment of various Mediator subunits as determined by ChIP-chip using epitope (Myc)-tagged Mediator subunits (green). Except for the last trace, all ChIPs were hybridized (and therefore normalized) against input DNA as in a. The last profile, however, shows an experiment were the MED15-Myc ChIP sample was hybridized (and therefore normalized) against a control ChIP sample performed using the same anti-Myc antibody but from an isogenic non-tagged strain. (d) TFIIB enrichment as determined by ChIP-chip using a rabbit polyclonal anti-TFIIB antibody (purple) as well as using a control IgG antibody (black) as in a. The middle panel shows TFIIB enrichment after subtracting the signal from the control (black) experiment. Overall, these experiments show that ChIP experiments tend to enrich highly transcribed coding regions regardless of the antibody used. It also shows that most of this systematic error can be removed either by normalizing against controls ChIPs performed in a non-tagged strain (in the case where a tagged protein is tested) or against a control ChIP performed using IgG (when a polyclonal antibody is used). Because each antibody varies with regards to the amount of noise it generates, we favor, when possible, using the "tagged versus non-tagged" strategy.

Supplementary Figure 2 A complement to Figure 1.

(a) A heat map representation of the data from Figure 1a. Genes were sorted by decreasing Rpb3 occupancy and the data were aligned on the TSS. (b) The average TFIIB (purple), RNAPII (Rpb3, red) and Mediator (Gal11, green) occupancies are shown around the TSS of RP genes. (c) Same as in b but for a group of control genes chosen based on the fact that they exhibit similar transcription rates as the RP genes from b. (d) A heat map representation of Mediator (Gal11) occupancy over the same genes as in b and c.

Supplementary Figure 3 A complement to Figure 3.

(a-c) Average Mediator (Gal11, green) occupancy in wild type (WT, solid traces) and the indicated CTD kinase mutants (dotted and dashed traces) around the TSS of all genes with an Rpb3 average ORF occupancy >1 in WT cells. TFIIB (purple) from WT cells is shown as a place-holder for core promoters. Data are shown for kin28-as mutant treated with NAPP1 (n=266) (a), ctk1Δ and bur2Δ mutants (n=299) (b) and srb10Δ mutant (n=295) (c). (d) Average Mediator (Gal11, green) and RNAPII (Rpb3, red) occupancy in wild type (WT, solid traces) and kin28-as mutant (kin28-as, dotted traces) cells, both treated with NAPP1, around the TSS for groups of genes with different RNAPII occupancies. The genes were grouped based on the average Rpb3 enrichment (log2 ratio) over their ORF (>1.5, Very high n=142; 1-1.5, High n=135; 0.5-1, Medium n=337; 0-0.5, Low n=827; <0, Very low n=1764).

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Jeronimo, C., Robert, F. Kin28 regulates the transient association of Mediator with core promoters. Nat Struct Mol Biol 21, 449–455 (2014). https://doi.org/10.1038/nsmb.2810

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