The carboxy-terminal domain (CTD) of the RNA polymerase II (RNAP II) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodelling. Here we show that a CTD arginine residue (R1810 in human) that is conserved across vertebrates is symmetrically dimethylated (me2s). This R1810me2s modification requires protein arginine methyltransferase 5 (PRMT5) and recruits the Tudor domain of the survival of motor neuron (SMN, also known as GEMIN1) protein, which is mutated in spinal muscular atrophy. SMN interacts with senataxin, which is sometimes mutated in ataxia oculomotor apraxia type 2 and amyotrophic lateral sclerosis. Because POLR2A R1810me2s and SMN, like senataxin, are required for resolving RNA–DNA hybrids created by RNA polymerase II that form R-loops in transcription termination regions, we propose that R1810me2s, SMN, and senataxin are components of an R-loop resolution pathway. Defects in this pathway can influence transcription termination and may contribute to neurodegenerative disorders.
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We thank J. Manley for GST–CTD constructs; D. Reinberg for RNAP II me2a antibodies; D. Eick for wild-type and RNAP II (R1810A) constructs; and S. Leppla for purified S9.6 antibodies. We also thank D. Torti and D. Leung for Illumina library preparation and sequencing, T. Hajian for the purified PRMT5–WDR77 complex, J. Li for purified 8WG16 antibodies, and D. Durocher for constructive criticism and advice during the course of this work. This project was supported by the Ontario Research Fund from the Ontario Ministry of Research and Innovation (to J.F.G. and T.P.) and by CIHR Operating Grants to J.F.G. and B.J.B. D.Y.Z. was supported by a National Science and Engineering Research Council of Canada Studentship and an Ontario Graduate Scholarship. U.B. was supported by a long-term Postdoctoral Fellowship from HFSP. B.J.B. holds the University of Toronto Banbury Chair in Medical Research.
The authors declare no competing financial interests.
Extended data figures and tables
Extended Data Figure 1 The R1810me2s and R1810me2a modifications on POLR2A depend on PRMT5 and CARM1, respectively.
a, POLR2A carries Rme2a and Rme2s modifications. Whole-cell lysates (WCL) from HEK293 cells stably expressing Flag-tagged TDRD3 or the POLR2D subunit of RNAP II were used for immunoprecipitation using beads conjugated with M2 anti-Flag antibody, and the precipitates were western blotted with the indicated antibodies. Cells expressing Flag–GFP were used as a negative control. Precipitated TDRD3 and POLR2D contained POLR2A with the Arg-me2a modification (ASYMM24 antibody), whereas precipitated POLR2D, and not TDRD3, contained POLR2A with the Arg-me2s modification (SYMM10 and Y12 antibodies). b, Whole-cell lysate western blot controls for Figure 1b. c, Y12 and R1810me2s recognition of RNAP II CTD R1810me2s is blocked by surrounding phosphorylated residues. The detection of R1810me2s improves for both antibodies when the precipitated samples are treated with alkaline phosphatase. d, Slot blots illustrating that the Y12 and R1810me2s antibodies specifically recognize peptides containing RNAP II R1810me2s. The indicated amounts of biotin-labelled 7mer CTD peptides bracketing R1810 with no modification, Arg-me2a, and Arg-me2s were blotted before incubating with the R1810me2s or Y12 antibodies. e, Western blot confirming efficient PRMT5 knockdown, and RT–qPCR assay confirming efficient CARM1 knockdown for experiment of Fig. 1c. f, g, Whole-cell lysate western blot controls for Fig. 1c,d, respectively. h–j, Whole cell lysate western blot controls for Fig. 3c–e, respectively.
a–c, In vitro fluorescence polarization (FP) peptide binding assays. a, Recombinant SMN Tudor domain was incubated with FITC-labelled 13-mer CTD peptides bracketing either R1810 or R1603. SMN preferentially bound CTD peptides in the order R1810me2s > R1603me2s ~ R1810me2a > R1603me2a, and exhibited no detectable affinity for the unmodified peptides. b, Recombinant SMN Tudor domain was incubated with FITC-labelled CTD peptides bracketing R1810me2s also containing Y1P, S2P or both upstream of R1810me2s, showing slightly preferential binding to the peptides when the phospho-modification(s) are present. c, FITC-CTD R1810me2s or FITC-CTD R1810me2a is not recognized by other recombinant Tudor domains from SMNDC1 (also known as SPF30), TDRD1, TDRD2, TDRD9 or TDRD11 (also known as SND1). d, Isothermal titration calorimetry assays showing that the recombinant SMN Tudor domain has no enhanced binding to R1810me2s containing peptides also carrying S2P or both Y1P and S2P.
a, PRMT5 overexpression increases the R1810me2s modification and the SMN and senataxin associations with RNAP II. Left, western blots with the indicated antibodies of HEK293 whole-cell lysates overexpressing Flag-tagged PRMT5 or GFP. Overexpressing PRMT5 does not increase the amount of SMN or senataxin. Right, endogenous POLR2A was immunoprecipitated (N20 antibody) from HEK293 cell lysates with overexpressed Flag-tagged PRMT5 or GFP. b, SMN associates with phospho-isoforms of RNAP II. Immunoprecipitation with SMN antibody, but not control IgG, co-precipitated RNAP II with unmodified CTD repeats (8WG16 antibody) and CTD repeats phosphorylated on Ser5 and Ser2 as detected by western blotting. c, Requirement of PRMT5 for association of SMN and senataxin with RNAP II. Left, western blots with the indicated antibodies of HEK293 whole-cell lysates expressing siRNAs for PRMT5 or SMN. Right, endogenous POLR2A was immunoprecipitated (N20 antibody) from cells with transient siRNA-mediated knockdown of PRMT5 or SMN. Western blots were performed with the indicated antibodies. PRMT5 knockdown causes loss of R1810me2s on POLR2A, as well as reduced association of SMN and senataxin with RNAP II. SMN knockdown causes reduced association of senataxin with RNAP II. d, SMN ChIP-seq (with GFP antibody against inducible GFP–SMN, or with SMN-specific antibody in HEK293 cells). Both methods observe enriched SMN signals at promoter and termination regions; the average of both is shown.
a, Chromatin immunoprecipitation (ChIP) was used to determine the distribution of SMN along the human GAPDH gene in HEK293 cells, expressed as percent input or as a ratio of SMN to RNAP II. Error bars represent technical variation in a single experiment (mean ± s.e.m., n = 3). b, SMN ChIP was performed in HEK293 cells stably expressing shRNAs for PRMT5 or GFP (as a control). With the control normalized to 1, knockdown of PRMT5 caused strong reductions of the SMN ChIP signals all along GAPDH. Error bars represent biological replicates (mean ± s.e.m., n = 3). c, SMN ChIP signals on GAPDH decrease in Raji cells expressing HA-tagged R1810A mutant POLR2A after 3 days of treatment with α-amanitin to eliminate endogenous POLR2A. ChIP results with wild-type HA-tagged POLR2A were normalized to 1. Error bars represent biological replicates (mean ± s.e.m., n = 3). d, ChIP in HEK293 cells showing the distribution of senataxin along the human GAPDH gene, expressed as percent input or as a ratio to RNAP II. Error bars represent technical variation in a single experiment (mean ± s.e.m., n = 3). e, Senataxin ChIP signals on GAPDH decrease in the POLR2A (R1810A) mutant after 3 days of treatment of Raji cells with α-amanitin to eliminate endogenous POLR2A. Results are normalized to wild-type POLR2A and expressed as the ratio of senataxin to RNAP II. Error bars represent biological replicates (mean ± s.e.m., n = 3). f, Knockdown of PRMT5 or SMN causes reductions of the senataxin ChIP signals all along GAPDH. ChIP against senataxin was performed in HEK293 cells with shRNA-mediated knock-down of PRMT5 or SMN. Results were normalized to a control knockdown of GFP and expressed as the ratio of senataxin to RNAP II. Error bars represent biological replicates (mean ± s.e.m., n = 2).
Extended Data Figure 5 The R1810 mutation causes RNAP II to accumulate in the termination region of ACTB.
Chromatin immunoprecipitation (ChIP) with three different POLR2A antibodies (8WG16, H224, 4H8), as indicated, was performed on the ACTB gene in Raji cells expressing HA-tagged wild-type or mutant (R1810A) POLR2A, 3 days after treatment with α-amanitin to eliminate endogenous POLR2A. Shown are single experiments with error bars representing technical variation (mean ± s.e.m., n = 3).
a, Chromatin immunoprecipitation (ChIP) with the N20, 4H8, and 8WG16 antibodies to show the distribution of wild-type POLR2A along the human GAPDH gene. Error bars represent technical variation (mean ± s.e.m., n = 3). b, POLR2A ChIP along the GAPDH gene was performed in HEK293 cells after stable knockdown of PRMT5 or SMN, using stable knockdown of GFP as a negative control. RNAP II over-accumulates at the termination sites on GAPDH after knockdown of PRMT5 or SMN. Error bars represent biological replicates (mean ± s.e.m., n = 5). c, POLR2A ChIP on the GAPDH gene was performed in Raji cells that express HA-tagged wild-type or mutant (R1810A) POLR2A 3 days after α-amanitin treatment to eliminate endogenous POLR2A. R1810A mutant RNAP II over-accumulates downstream of the cleavage and polyadenylation sites where RNAP II pauses and terminates transcription on GAPDH. Error bars represent biological replicates (mean ± s.e.m., n = 4). d, Data from b, c are displayed as normalized ratios to the control (GFP knockdown, or HA wild-type POLR2A), with the ratio for the intron 5 qPCR primers at 2436 set as 1. e, Nuclear run-on experiment in which nuclei from Raji cells expressing wild-type or mutant (R1810A) POLR2A 3 days after α-amanitin treatment to eliminate endogenous POLR2A were incubated with BrUTP for 30 min, and short run-on RNAs were isolated by binding to anti-BrU antibodies. The R1810A mutation led to over-accumulation of active RNAP II in the region downstream of the poly(A) site on GAPDH. Error bars represent technical variation (mean ± s.e.m., n = 3).
Extended Data Figure 7 PRMT5 and SMN but not CARM1 regulate transcription termination by RNAP II on ACTB and GAPDH.
a, Chromatin immunoprecipitation (ChIP) for POLR2A with 4H8 antibody was performed after stable shRNA-mediated PRMT5, CARM1 or SMN knockdown in HEK293 cells to show that only PRMT5 and SMN knockdowns lead to the over-accumulation of RNAP II in the termination regions of ACTB. The graph shows a single experiment with error bars representing technical variation (mean ± s.e.m., n = 3). b, POLR2A ChIP with the 8WG16 antibody was performed after transient siRNA-mediated knockdown of PRMT5 or SMN in HEK293 cells to show that PRMT5 or SMN knockdown leads to the over-accumulation of RNAP II in the termination region of β-actin. The graph shows a single experiment with error bars representing technical variation (mean ± s.e.m., n = 3). c, ChIP for POLR2A with 4H8 antibody was performed after stable shRNA-mediated knockdown of PRMT5, SMN or GFP (as a control) in HEK293 cells to show that knockdown of PRMT5 or SMN leads to the over-accumulation of RNAP II in the termination region of GAPDH. The graph shows a single experiment with error bars representing technical variation (mean ± s.e.m., n = 3). d, POLR2A ChIP with 8WG16 antibody was performed after transient siRNA-mediated knockdown of PRMT5 or SMN in HEK293 cells to show that knockdown of PRMT5 or SMN leads to the over-accumulation of RNAP II in the termination region of GAPDH. The graph shows a single experiment with error bars representing technical variation (mean ± s.e.m., n = 3).
Extended Data Figure 8 RNAP II pausing defect and R-loop accumulation are observed in CRISPR SMN knockout cells and in SMA disease cells.
a, ChIP for POLR2A with N20 antibody was performed after stable SMN knockout (CRISPR) in HEK293 cells shows that RNAP II accumulates in the termination regions of ACTB. Scrambled guide RNA treatment was used as a negative control. Error bars represent biological variation (mean ± s.e.m., n = 3). b, Accumulation of R-loops in the termination regions of the ACTB gene after SMN knockout. A fusion protein of GFP–RNase H DNA–RNA hybrid binding domain was stably expressed in HEK293 cells. ChIP with GFP antibody (Abcam 290) was used for the detection of the R-loops (DNA–RNA hybrids), using the indicated primer positions for qPCR along the gene. Scrambled guide RNA treatment was used as a negative control. Error bars represent biological variation (mean ± s.e.m., n = 3). c, Top: live cell microscopy images showing that HEK293 cells with SMN knockout appear to be physiologically normal in comparison to the control scrambled KO. Bottom: western blot with anti-SMN antibody showing that SMN expression is knocked out by CRISPR. d, Human cell lines (3 fibroblast, 3 B lymphocyte) were obtained from the Coriell Institute for Medical Research. These include cells from two children with SMA disease and their normal parents. e, ChIP for POLR2A (N20, 8WG16 antibodies) was performed on the ACTB gene using the averaged value of the parents as control. POLR2A in the SMA disease cells (from both fibroblast and B cell lines) accumulates in the termination regions of the ACTB gene. Error bars represent biological variation (mean ± s.e.m., n = 4). f, Top: quantification of R-loops by DNA immunoprecipitation (DIP) with the S9.6 antibody in the patient cells, showing that the R-loops are sensitive to RNase H. Error bars represent technical variation (mean ± s.e.m., n = 3). Bottom: R-loop DIP with the S9.6 antibody shows that R-loops accumulate in the termination regions of the ACTB gene in the SMA disease cells. The averaged value of the parents was used as a control. Error bars represent biological variation (mean ± s.e.m., n = 5).
Extended Data Figure 9 SMN and POLR2A(R1810) effects on transcription termination by RNAP II occur on a genome-wide level.
a, Western blot using N20 antibody for POLR2A and SMN antibody to verify shSMN knockdown of SMN for the ChIP-seq experiment of Fig. 4e; shGFP was used as a control. b, Western blot using N20 and HA antibodies to verify equal expression of HA-tagged wild-type and POLR2A(R1810A) and the effect of α-amanitin treatment on cells without an HA-tagged construct for the ChIP-seq experiment of Fig. 4e. c, RNAP II ChIP-seq results for several housekeeping genes are displayed in detail (B2M, CD40, ATF4 (a short gene), JUND (an intronless gene), and TUBA1B) using the Integrative Genomics Viewer. The promoter peaks are displayed to the left, and the regions underlined in red are RNAP II termination regions. IgG ChIPseq was used as negative control. Approximately 10 million unique RNAP II ChIPseq reads (4H8, 8WG16) were obtained from GFP or SMN stable knockdown Raji cells. Approximately 10–12 million unique RNAP II ChIP-seq reads (N20) were obtained from wild-type or R1810A POLR2A Raji cells upon 3 days of amanitin treatment (2 μg ml−1).
Extended Data Figure 10 Model of the pathway that regulates R-loop accumulation to prevent DNA damage.
a, b, Quantification of γH2AX:H2AX ratio through ChIP in HEK293 (a) or Raji (b) cells, along the ACTB gene, after knocking down PRMT5, or SMN, with GFP knockdown as a negative control (a), or mutating R1810 to alanine (b). Error bars denote s.e.m. (n = 4). c, Pathway (boxed) and model showing influence of PRMT5, R1810me2s, and SMN on R-loop resolution and transcription termination.
This file contains Supplementary Table 1 which shows the number of times each type of experiment described in this work was performed with the reported results) and raw western blots used in the paper. (PDF 1998 kb)
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Yanling Zhao, D., Gish, G., Braunschweig, U. et al. SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination. Nature 529, 48–53 (2016). https://doi.org/10.1038/nature16469
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