Chemical-genomic dissection of the CTD code

Abstract

Sequential modifications of the RNA polymerase II (Pol II) C-terminal domain (CTD) coordinate the stage-specific association and release of cellular machines during transcription. Here we examine the genome-wide distributions of the 'early' (phospho-Ser5 (Ser5-P)), 'mid' (Ser7-P) and 'late' (Ser2-P) CTD marks. We identify gene class-specific patterns and find widespread co-occurrence of the CTD marks. Contrary to its role in 3'-processing of noncoding RNA, the Ser7-P marks are placed early and retained until transcription termination at all Pol II-dependent genes. Chemical-genomic analysis reveals that the promoter-distal Ser7-P marks are not remnants of early phosphorylation but are placed anew by the CTD kinase Bur1. Consistent with the ability of Bur1 to facilitate transcription elongation and suppress cryptic transcription, high levels of Ser7-P are observed at highly transcribed genes. We propose that Ser7-P could facilitate elongation and suppress cryptic transcription.

Figure 1. Pol II and CTD Phosphorylation Profiles

(a) ChIP-chip profiles for representative genes chosen to display the diversity of Pol II profiles across the genome. Pol II is shown in blue and total RNA is shown in black. Translation boundaries are indicated by the black boxes, and transcription boundaries shown as an arrow (Transcription Start Site, TSS) and a red bar (Cleavage and Polyadenylation Site, CPS). Introns are marked with a ^ symbol. Scale on x-axis corresponds to distance in base pairs from the TSS. Scale on y-axis represents fold enrichment of IP over input on a Log₂ scale for ChIP-chip data and fold expression over background for total RNA data. The cartoon beneath the plots illustrates the potential Pol II distributions that would yield the observed ChIP-chip occupancy profiles. (b) ChIP-chip profiles of genes for which Pol II occupancy profile (blue) is constant across the ORF. Phosphorylation profiles are shown in purple (Ser7-P), red (Ser5-P), and green (Ser2-P) and total RNA is shown in black.

Figure 2. Genome-wide Pol II and CTD Phosphorylation Profiles

(a) The diagram summarizes the scale used in the average transcription unit analysis. Bins within transcribed region are equivalent to 10% of the transcribed region length and bins flanking this region (−1, +1) are a constant 157bp. (b) Representative clusters from the K-means clustering analysis for Pol II, Ser7-P, Ser5-P, and Ser2-P occupancy profiles across the genome using average transcription unit analysis (see Methods). U: uniform enrichment across the transcription unit; 5: 5’ enrichment; 3: 3’ enrichment ; 5+3: or 5’ and 3’ enrichments. The dominant profile(s) for each is highlighted. (c) Pie chart diagrams displaying the distribution of genes within each gene set for Pol II, Ser7-P, Ser5-P, and Ser2-P having each of the profiles shown in (b). Set I –Annotated protein-coding genes (6147 genes); Set II – pc-genes with an average Pol II enrichment in the top 10% (615 genes); Set III –pc-genes isolated by 400bp and having an average Pol II enrichment greater than or equal to 1 (60 genes). (d) Histogram of significantly enriched gene ontology (GO) categories within individual Ser7-P clusters (U, 5, 3, and 5+3). Details for each GO category are provided in Supplementary Table 1. (e) Box plots of transcription frequency for genes within each Ser7-P cluster . The uniform (U) Ser7-P cluster is strongly enriched for genes with higher rates of transcription frequency compared to the genome average (P-value = 3.35 × 10⁻³⁰). (f) Bar graph of transcription machinery at the upstream activating sequence (UAS) within individual Ser7-P clusters. The individual proteins are listed in Supplementary Fig. 6. Proteins that are enriched within the cluster are represented by positive values, while proteins that are depleted are represented by negative values . Dashed lines segregate the components of each complex.

Figure 3. CTD Phosphorylation Profile for Protein-coding and Non-coding Genes

(a) Phosphorylation profiles across several representative nc-genes (left column) and pc-genes (right column). Color-coded arrows indicate the respective phosphorylation peak. The nc-genes display overlapping Ser5-P (red) and Ser7-P (purple) profiles, while varying levels of 3’ Ser7-P enrichment is observed in pc-genes. Ser2-P (green) appears to be less abundant in nc-genes. The nucleosome positions near the TSS are displayed as orange circles (drawn to scale). (b) Histograms displaying the relative enrichment (with respect to Pol II levels) across nc- and pc-genes for Ser7-P and Ser2-P. The Ser2-P levels are significantly lower in nc-genes than pc-genes (P-value = 4.4×10⁻²¹). No significant difference in Ser7-P was detected between nc-genes and pc-genes (P-value = 0.658).

Figure 4. Small Molecule Inhibition of CTD Phosphorylation

(a) Inhibition effects on total RNA (black), Pol II (blue), Ser7-P (purple), Ser5-P (red), and Ser2-P (green) occupancy profiles for SED1. Uninhibited profiles are shown as a solid line and inhibited profiles shown with a dashed line. (b) Summary of average Kin28as+Srb10as responses to inhibition for Pol II (blue), Ser7-P (purple), Ser5-P (red), and Ser2-P (green). Data displayed for 415 genes with “uniform” Pol II profiles from Set II in the Wild Type strain (see Supplementary Fig. 11, central Pol II Pie). The solid and dashed lines indicate the uninhibited and inhibited Kin28as+Srb10as average profiles, respectively. Scale on the x-axis is shown as distance from the TSS using average transcription unit analysis (described in Fig. 2a). Scale on y-axis represents fold enrichment of IP over input on a Log₂ scale. (c) Comprehensive diagrams displaying the comparison between the uninhibited wild type strain (large central pies) and the inhibited double mutant strain (smaller pies) for all the genes in Set III (described in Fig. 2c). Summaries shown for Pol II (blue), Ser7-P (purple), Ser5-P (red), and Ser2-P (green). The smaller pie charts correspond to a slice of the wild type chart and show the partitioning of the genes from the double mutant data within that slice after the inhibitor was added. The profiles U, 5, 3, and 5+3 are as described in Figure 2 and “I” is used to indicate the profiles seen after inhibition (I^U, I⁵, I³, and I⁵⁺³).

Figure 5. Promoter-Distal Ser7-P Marks are Not Remnants of Promoter-Proximal Kin28 Phosphorylation

(a) Ser7-P marks within the coding region are not remnants of phosphorylation at the promoter. The Kin28as+Srb10as strain was treated for 60 min with DMSO or the inhibitors 1-NA-PP1/1-NM-PP1 under non-inducing conditions. The GAL genes were induced for 30 minutes, and ChIP-qPCR was performed against the 5' and 3' ends of the GAL1 genes (black bars indicate primer location). Upon inhibition, Ser7-P was significantly reduced at the 5' end but not the 3' end of GAL1. (b) Representative ChIP-chip profiles for Ser5-P (red) and Ser7-P (purple) at a nc-gene polycistronic cluster (SNR78-72) and a pc-gene (GLN1) demonstrating the effects of Kin28 and Srb10 inhibition. The inhibition of Ser5-P is observed predominantly at the 5’ ends of both nc- and pc-genes. At nc-genes, the total level of Ser7-P decreases uniformly across the transcript, while at pc-genes the primary effect of the inhibition is seen at the 5’ end of the transcript. This suggests the presence of a secondary Ser7 kinase acting near the 3’ end of pc-genes (indicated by a *). (c) Histogram demonstrating the effects of inhibition on the relative Ser7-P enrichment (with respect to Pol II levels) at the 3’ end of the ORF at of nc-Genes (left panel) and pc-Genes (right panel). (nc-genes: P = 1.2×10⁻⁶; pc-genes: P = 0.716)

Figure 6. Bur1 Kinase Directly Phosphorylates Ser7

(a) Kinase assay using a GST-CTD₄ and GST-CTD₁₄ substrates and purified Cka1, Kin28, and Bur1 kinases. The blots were probed with antibodies against Ser5-P (top) and Ser7-P (bottom). (b) ELISA of GST-CTD₄ phosphorylated by purified yeast kinases and probed with antibodies against Ser7-P (purple), Ser5-P (red), and Ser2-P (green). (c) Dot blot of GST-CTD₁₄ phosphorylated by Bur1 and the analog-sensitive mutant Bur1as (Bur1-L149G) probed with anti-Ser7-P antibodies. (d) Ser7-P enrichment profile (normalized to Pol II) across the YRA1 gene showing the effects of inhibition of either Kin28as+Srb10as or Bur1as. (e) Average Pol II (blue) and Ser7-P (purple) from uninhibited (solid line) and inhibited (dashed lines) Bur1as cells at 415 genes with uniform and robust Pol II occupancy from Set II (top panels). Pol II normalized fold change in Ser7-P across the same subset of genes (bottom panel) is shown to highlight the role of Bur1 in Ser7 phosphorylation across the transcribed unit. (f) Distribution of average Pol II normalized fold changes in Ser7-P within a 10% window centered around the TSS and the 3’ ORF boundary of Set III genes. Distributions from Kin28as+Srb10as and Bur1as cells were compared using a two-sided student's T-test.