Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

Abstract

Termination of RNA polymerase II (Pol II) transcription is a key step that is important for 3' end formation of functional mRNA, mRNA release, and Pol II recycling. Even so, the underlying termination mechanism is not yet understood. Here, we demonstrate that the conserved and essential termination factor Seb1 is found on Pol II near the end of the RNA exit channel and the Rpb4/7 stalk. Furthermore, the Seb1 interaction surface with Pol II largely overlaps with that of the elongation factor Spt5. Notably, Seb1 co-transcriptional recruitment is dependent on Spt5 dephosphorylation by the conserved PP1 phosphatase Dis2, which also dephosphorylates threonine 4 within the Pol II heptad repeated C-terminal domain. We propose that Dis2 orchestrates the transition from elongation to termination phase during the transcription cycle by mediating elongation to termination factor exchange and dephosphorylation of Pol II C-terminal domain.

Keywords: C-terminal domain; CID; CTD; CTD interacting domain; CTD phosphorylation; PP1 phosphatase; RNA polymerase II; Spt5; transcription termination.

Graphical abstract

Figure 1

Differential Distribution of Phospho-Marks on Protein-Coding Genes (A) Averaged occupancy profiles of Pol II (8WG16), phospho-Pol II, and input from ChIP-seq on all 4,105 yeast protein coding-genes (upper panel). Color-coded heatmaps illustrating the phospho-Pol II profiles across single genes (lower panel). Profiles are aligned to the TSS (transcription start site) and PAS (polyadenylation site) as indicated. (B and C) ChIP-seq profiles across rpl1202 (B) and anc1 (C) genes.

Figure 2

Dis2 Is a Thr4P Phosphatase (A) Deletion of dis2 or expression of the phosphatase-defective dis2-R245Q allele increase the level of Thr4P. Whole-cell extracts were analyzed by western blot using antibodies specific for Thr4P, Tyr1P, Ser2P, Ser5P, Ser7P, and Pol II (8WG16). (B) Silver-stained SDS-PAGE analysis of Pol II, Dis2, and Dis2 R245Q purified from yeast. (C) Purified Pol II was incubated with Dis2, and levels of phosphorylated Pol II were assessed by western blot using antibodies specific for Thr4P, Tyr1P, Ser2P, and Ser5P. (D) Purified Pol II was incubated with Dis2 or Dis2 R245Q, and levels of Thr4P Pol II were assessed by western blot with anti-CTD and Flag antibodies. See also Figure S1.

Figure 3

Increased Thr4P Downstream of PAS upon Loss of Dis2 Coincides with Transcription Termination Defect (A and B) Spike-in normalized ChIP-seq meta-profiles of Thr4P (A) and Pol II-8WG16 (B) around the PAS over a set of 1,735 representative non-overlapping protein-coding genes (see STAR Methods), averaged from two biological replicas. (C and D) Thr4P and Pol II profiles across rpl1202 (C) and anc1 (D) genes. (E) Results from a tetrad dissection of heterozygous T4A-CTD (left) and T4E-CTD (right) mutants. Three dissections are shown. See also Figure S2.

Figure 4

Lack of Dis2 Activity Leads to Global Decrease of the Termination Factor Seb1 (A–C) Spike-in normalized ChIP-seq meta-profiles of Pcf11 (A), Rhn1 (B), and Seb1 (C) around the PAS, averaged from two biological replicas. Protein-coding genes for analysis were selected as above (n = 1,735). (D) Pcf11, Rhn1, and Seb1 profiles on individual genes. (E) Binding of SUMO-Pcf11-CID to the FAM-tagged two-repeat non-phosphorylated or phosphorylated CTD peptides measured by FA. Error bars show the SD of two technical repeats. (F) FA assay for Seb1-CID. Error bars show the SD of two technical repeats. See also Figures S3 and S4 and Table S1.

Figure 5

Seb1 Competes with Spt5 for Binding to Pol II (A) SDS-PAGE analysis of the purified recombinant Seb1, Pol II, reconstituted Pol II-Seb1 complex, and Pol II-Seb1 complex cross-linked with BS3. (B) Pol II crystal structure with Spt4/5 (PDB ID: 5XON) showing mapped positions of lysine-lysine cross-links (green spheres) between fission yeast Pol II subunits and Seb1. (C) SDS-PAGE analysis of Pol II before and after tobacco etch virus (TEV) cleavage. (D) Ion-exchange purification of CTD-less Pol II. (E) SDS-PAGE analysis of the purified recombinant Spt4/5. (F) The Pol II-Spt4/5 complex was incubated with increasing amount of recombinant purified Seb1. The competition between Seb1 and Spt5 for Pol II binding was analyzed by western blot with antibodies specific for Seb1 (His), Spt5 (His), and Pol II subunit Rpb9 (Flag). See also Figure S5 and Table S2.

Figure 6

Spt5 T1A Rescues Seb1 Recruitment (A and B) Spike-in normalized ChIP-seq meta-profiles of Seb1 around the PAS in dis2⁺, spt5 wt and dis2Δ, spt5 wt/T1A/T1E (A) or dis2⁺, spt5 wt/T1A/T1E (B) from four biological replicas (dis2⁺, spt5 wt/T1E and dis2Δ, spt5 wt/T1A/T1E) or three biological replicas (dis2⁺, spt5 T1A). Protein-coding genes for analysis were selected as above (n = 1,735). The black solid line defines the position of ChIP-seq peak in the WT (dis2⁺spt5 wt) strain. (C) Quantitation (boxplots) of Seb1 ChIP signal from (A) and (B). (D) Analysis of termination defects on the rpl1202 gene. Position of the RT-PCR products is shown in the schematic. Data are represented as mean ± SEM. (E and F) Spike-in normalized ChIP-seq meta-profiles of total Pol II (8WG16) around the PAS in dis2⁺, spt5 wt and dis2Δ, spt5 wt/T1A/T1E (E) or dis2⁺, spt5 wt/T1A/T1E (F) averaged from two biological replicas. Protein-coding genes for analysis were selected as above (n = 1,735). The normalized profiles were horizontally translated to have approximately equal occupancy levels upstream of the PAS. The black solid line defines the position of ChIP-seq peak in the WT (dis2⁺, spt5 wt) strain. See also Figure S6.

Figure 7

Model PP1-Dis2 dephosphorylates Spt5 and CTD-Thr4P at the end of the transcription cycle (WT). Upon depletion of PP1, hyper-phosphorylation of both Spt5 and Thr4P causes defects in transcription termination (no PP1).