Functional association of Gdown1 with RNA polymerase II poised on human genes

Abstract

Most human genes are loaded with promoter-proximally paused RNA polymerase II (Pol II) molecules that are poised for release into productive elongation by P-TEFb. We present evidence that Gdown1, the product of the POLR2M gene that renders Pol II responsive to Mediator, is involved in Pol II elongation control. During in vitro transcription, Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. Supporting these mechanistic insights, ChIP-Seq demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Our results establish that Gdown1 stabilizes poised polymerases while maintaining their responsiveness to P-TEFb and suggest that Mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function.

Figure 1. Gdown1 inhibits the function of TFIIF

(A) Isolated EECs were supplemented with indicated amounts of bovine or human Gdown1 and further elongation was performed for 2 min. in the absence or presence of 0.1 pmole TFIIF. The autoradiograph shows labeled transcripts analyzed in a 6% TBE/urea gel. (B) Isolated EECs were either left untreated or incubated with 1 pmole Gdown1 for 3 min. at room temperature. After the incubation, the EEC(G)s were reisolated either with a low salt wash (LSW) or with a high salt wash (HSW) for 5 min. Then EECs or reisolated EEC(G)s were further elongated for 2 min. in the absence or presence of 0.1 pmole TFIIF. (C) Analysis of ECC•Gdown1 interaction using EC-EMSA. Isolated EECs were released from the beads through a restriction enzyme digestion and then incubated with indicated amounts of Gdown1. In lanes 7 and 8, EEC(G)s were formed, reisolated by a high salt wash, and then released by a restriction enzyme digestion. The samples were then subjected to analysis on a native gel. (D) EECs or EEC(G)s were incubated with the indicated factors and then analyzed by EC-EMSA. In lanes 6 and 7, TFIIF was added prior to the addition of Gdown1. Asterisks (*) in B, C, and D signify that the indicated amounts of Gdown1 were incubated with EECs to form EEC(G) before reisolation.

Figure 2. Gdown1 affects the functions of DSIF and NELF, but not HCE or TFIIS

(A) Isolated EECs or EEC(G)s (as described in the Figure 1 legend if Gdown1 is indicated) were supplemented with combinations of DSIF and NELF before a 6 minute chase. (B) Isolated EECs were supplemented with Gdown1 and further elongation was performed for 1 minute in the absence or presence of 1 pmole HCE or TFIIS.

Figure 3. The effects of Gdown1 on Pol II elongation in the presence of HNE

(A). Isolated EECs were supplemented with Gdown1, HNE, 1 pmole P-TEFb or 1 μM FP as indicated and further elongation was performed for 3 min. Transcription elongation was then stopped and an aliquot was taken from each reaction to show the pattern of transcripts for the total reaction (“T”). Another aliquot was separated into a supernatant fraction (“S”) and a bead bound fraction (“B”). (B) Isolated EECs were supplemented with 1 pmole Gdown1 and/or TTF2. Elongation complexes were either incubated with 0.5 mM ATP for 5 min. at room temperature (lanes 1-5) or further elongated for 5 min. upon the addition of 0.5 mM NTP (lanes 6-11). After the incubation or elongation reactions were done, the supernatant fractions in the indicated reactions were separated from the beads.

Figure 4. Negative effect of TFIIS and the influence of other factors on Gdown1

(A) EECs or EECs with Gdown1, EEC(G)s, were incubated with factors or extract and allowed to elongate for 6 min. in the presence of increasing amounts of TFIIS (0, 0.5, 1.5 or 5 pmole). (B) The effects of TFIIS (S) and TFIIF (F) were examined on the indicated elongation complexes. Elongations complexes were EECs or EEC(G)s. Abortive elongation complexes, AEC(G)s, are EEC(G)s in the presence of a HNE with FP. Productive elongation complexes are EEC(G)s incubated with HNE, extra P-TEFb and ATP for 5 minutes and then chased in the presence of FP. Elongation complexes were washed with 1.6 M salt (HSW) before the chase. Chases were for 6 min. and contained the indicated elongation complexes alone or were supplemented with TFIIS, or TFIIF. Details are present in the Experimental Procedures and in the text. The asterisk above lane 13 in A signifies that although no TFIIS was added, the extract present does contain TFIIS.

Figure 5. ChIP-Seq analyses of Pol II and Gdown1

Pol II and Gdown1 occupancy in HeLa cells was determined by ChIP-Seq analysis as described in Experimental Procedures. Vertical axis indicates occupancy normalized for the total number of reads obtained (counts per 1 million reads). (A), (B), and (C) show density of Pol II and Gdown1 across indicated human genes. Pol II occupancy was determined in cells treated with FP for 0, 5, or 60 minutes. Gdown1 occupancy was determined in cells treated with FP for 0 or 60 minutes. (D) Pol II and Gdown1 binding from -2 kb to +2 kb around the TSS of top 20,000 RefSeq genes without TSSs within 1000 bp of any other TSS, rank ordered from most Pol II bound to least Pol II bound. The high resolution heatmaps for Pol II and Gdown1 were generated as described in Experimental Procedures. (E) Ratio of Gdown1 to Pol II for the region from -500 to +500 around the TSS of 5000 genes rank ordered by the amount of Pol II. Dots are individual ratios for each gene and the thick line is a running average (100 points each).

Figure 6. Global ChIP-Seq analysis of Pol II and Gdown1

Average gene data for a customized set of 24,160 RefSeq genes, from which all genes with TSSs within 1000 bp of each other have been excluded, were analyzed as described in the text and the Experimental Procedures. The three views depict relative signals in the indicated regions around the TSSs after averaging, background subtraction, and normalization of the entire -10,000 to +10,000 region (see Figure S4). The vertical scale in right hand panel was expanded 10-fold compared to other two panels. (A) Indicated regions for Pol II from control (red) and FP treated (blue) cells. (B) Indicated regions for Gdown1 from control (purple) and FP treated (green) cells. (C) Indicated regions for Pol II from control siRNA (red) and Gdown1 siRNA treated (black) cells.

Figure 7. Effect of FP on position of Gdown1

Peaks of Pol II and Gdown1 were identified using the program ChIP-Seq Peak and displayed above the individual tracks for Pol II and Gdown1 from control cells or FP treated cells as indicated for the promoter regions of (A) PPP1R10 and MRPS18B, and (B) RPS20. An average position for identified peaks for 25,530 RefSeq genes was compiled as described in Experimental Procedures for (C) Pol II and (D) Gdown1 from control or FP treated cells.