SRSF10 Connects DNA Damage to the Alternative Splicing of Transcripts Encoding Apoptosis, Cell-Cycle Control, and DNA Repair Factors

Abstract

RNA binding proteins and signaling components control the production of pro-death and pro-survival splice variants of Bcl-x. DNA damage promoted by oxaliplatin increases the level of pro-apoptotic Bcl-xS in an ATM/CHK2-dependent manner, but how this shift is enforced is not known. Here, we show that in normally growing cells, when the 5' splice site of Bcl-xS is largely repressed, SRSF10 partially relieves repression and interacts with repressor hnRNP K and stimulatory hnRNP F/H proteins. Oxaliplatin abrogates the interaction of SRSF10 with hnRNP F/H and decreases the association of SRSF10 and hnRNP K with the Bcl-x pre-mRNA. Dephosphorylation of SRSF10 is linked with these changes. A broader analysis reveals that DNA damage co-opts SRSF10 to control splicing decisions in transcripts encoding components involved in DNA repair, cell-cycle control, and apoptosis. DNA damage therefore alters the interactions between splicing regulators to elicit a splicing response that determines cell fate.

Keywords: DNA damage response; DNA repair; RNA binding proteins; SR proteins; alternative splicing; apoptosis; cell cycle; cell fate; hnRNP proteins; oxaliplatin; phosphorylation; splicing.

Figure 1. SRSF10 Controls the Alternative Splicing of Bcl-x

Schematic representation of the human Bcl-x gene (BCL2L1) with relevant portions included in minigene X2, and the positions of the RT primer and PCR primer pairs used to carry RT-PCR assays. (B) Following RNAi in 293 cells with the indicated concentrations of siSRSF10, an immunoblot with anti-SRSF10 antibodies was carried out (top panel). The positions of the full–length (SRSF10-1) and truncated splice variant (SRSF10-2) are shown. RT-PCR assays performed on the endogenous Bcl-x transcripts; the separation of radio-labeled RT-PCR products is shown for one experiment in the middle panel, with the positions of the Bcl-xS and Bcl-xL products indicated. The histograms shown in the bottom panel represent the average production of Bcl-xS in percentage from triplicates with SDs. (C) Assay as in (B), except that 293 cells were transfected with the Bcl-x minigene X2, and the RT-PCR assay used a minigene-specific pair of primers. (D) Plasmids allowing expression of HA-SRSF10 and FLAG-SRSF10 were co-transfected with minigene X2. The impact on Bcl-x splicing was monitored as in (C). The CTRL sample was only transfected with X2, whereas pCDNA3.1 is an empty expression plasmid co-transfected with X2. (E) Schematic representation of the HA-SRSF10 and derivatives lacking various domains. (F) After transfection in 293 cells (quantity of plasmid transfected indicated in micrograms), the expression of HA-SRSF10 and derivatives was verified by immunoblotting using anti-HA antibody. (G) Samples of (F) were tested for Bcl-x splicing using the X2 reporter as described in (D). Error bars indicate SD. In all cases, asterisks represent significant p values (two-tailed Student's t test)comparing the means between samples and their respective controls; *p < 0.05, **p < 0.01, and ***p < 0.001.

Figure 2. SRSF10 Requires hnRNP F/H to Control Bcl-x Splicing and Interacts with hnRNP F, H, and K Proteins

(A) Schematic representation of regulatory elements surrounding the 5′ splice site of Bcl-xS. (B) The X2 minigene and derivatives were transfected either alone or with the HA-SRSF10 plasmid. RT-PCR assays were carried out, and radiolabeled RT-PCR products were fractionated on a non-denaturing gel to quantitate Bcl-xS and Bcl-xL products. The histograms represent the average percentage of Bcl-xS products from triplicate experiments. (C) siF/H was used to deplete hnRNP F/H with an immunoblot shown to verify depletion. HA-SRSF10 was transfected in 293 cells treated or not with siF/H. RT-PCR was carried out to detect the Bcl-x splice variants, as described in (B). (D) Immunoprecipitation assays using 293 cells transfected with FLAG-SRSF10. The material recovered was fractionated and transferred on nitrocellulose decorated with anti-FLAG antibodies. (E) siK was used to deplete hnRNP K and an immunoblot is shown. HA-SRSF10 was transfected in 293 cells treated or not with siK. RT-PCR was carried out to detect the Bcl-x splice products, as described in (B). (F) Immunoprecipitation assays with hnRNP K antibody. Using 293 cells transfected with FLAG-SRSF10, the recovered material was fractionated, transferred on nitrocellulose that was decorated with anti-FLAG antibodies. “xx” and “x” indicate the large and small immunoglobulin subunits that react with the secondary antibody, respectively. Error bars indicate SD. Asterisks represent p values (two-tailed Student's t test) comparing the means between samples and their respective controls; *p < 0.05, **p < 0.01, and ***p < 0.001.

Figure 3. The Bcl-x Splicing Shift Induced by Oxaliplatin Requires SRSF10 and hnRNP F/H, and Is Associated with the Loss of Interaction between SRSF10 and hnRNP F/H

(A) The X2 minigene and derivatives lacking different elements were transfected into 293 cells. Four hours later, cells were treated with oxaliplatin for 24 hr. The impact of oxaliplatin on Bcl-x splicing was determined by RT-PCR. (B) The role of hnRNP F/H was tested by depleting hnRNP F/H by RNAi. The top panel shows an immunoblot for hnRNP F. The middle and bottom panels show the results of the RT-PCR assays to detect endogenous Bcl-x transcripts. (C) The role of SRSF10 on the oxaliplatin-induced Bcl-x splicing shift was tested by depleting siSRSF10. The top panel confirms the depletion of SRSF10. The middle and bottom panels show the results of the RT-PCR assays on endogenous Bcl-x transcripts. (D) Immunoprecipitation of FLAG-SRSF10 was performed with anti-hnRNP F, H, and K antibodies using extracts prepared from cells treated or not with oxaliplatin, and expressing or not FLAG-SRSF10. The input content of FLAG-SRSF10 is shown and represents 1/50^th of the samples used for immunoprecipitation. Immunoprecipitates were fractionated on gel and proteins were transferred to nitrocellulose decorated with anti-FLAG antibodies. “xx” indicates the large immunoglobulin subunit used for the immunoprecipitation that reacts with the secondary antibody. (E) The immunoprecipitation assays used cells expressing SRSF10-FLAG, RS1-FLAG, or the RS2-FLAG treated or not with oxaliplatin. The procedure is as described in (D). Anti-K antibodies are from mouse, whereas anti-F and anti-H antibodies are from rabbit. A rabbit IgG was used for the control immunoprecipitation. “xx” and “x” indicate the large and small immunoglobulin subunits that react with the secondary anti-mouse antibody, respectively. (F) Immunoprecipitation was carried out on cells treated or not with oxaliplatin. The recovered RNA was quantitated for Bcl-x pre-mRNA using primers shown on the top. Raw data are provided in Table S1. The differential between values obtained for each antibody comparing the impact of oxaliplatin is plotted in histograms. The result obtained with IgG control immunoprecipitations is provided in Table S1. Also shown in Table S1 are the results obtained from two experiments comparing immunoprecipitations performed with cells treated with formaldehyde and untreated cells.

Figure 4. Schematic Model of the Proposed Role of SRSF10, hnRNP F/H, and hnRNP K in Bcl-x Pre-mRNA Splicing, and How Oxali-platin Reprograms Their Interactions

Repressor complex representing the major regulatory assembly in normally growing 293 cells. (B) Activating complex proposed to form on a minor fraction of Bcl-x transcripts in normally growing 293 cells or when SRSF10 is overex-pressed. (C) Impact of oxaliplatin on the interaction of regulatory components leading to the activation of the 5′ss of Bcl-xS.

Figure 5. Dephosphorylation of SRSF10 by Oxaliplatin

(A) Total cellular extracts were collected 24 hr after treatment or not with oxaliplatin. Aliquots of the untreated cellular extract were incubated with or without calf intestinal phosphatase (CIP) for 15 min at 37°C. Proteins were fractionated on gel and transferred to nitrocellulose to reveal SRSF10. (B) Amino acid sequence of the SRSF10-1 protein showing the different domains (RRM, RS1, and RS2) in differently shaded boxes. The regions of SRSF10 to which peptides identified by LC-MS/MS analysis mapped are underlined.(C) Proteins recovered from duplicate anti-FLAG immunoprecipitations using cells expressing FLAG-SRSF10 and treated or not with oxaliplatin were analyzed by LC-MS/MS analysis after trypsin digestion. Histograms depict the relative abundance of two SRSF10 peptides containing a phosphorylated serine compared to the respective unmodified versions. The peptide in the RS1 domain is shown in bold in (B), and the position of both serines is indicated. (D) Diagram of the mutated versions of HA-SRSF10 carrying either a deletion of S131, S133, or both. (E) The impact of mutated HA-SRSF10 on Bcl-x splicing was tested by co-transfecting minigene X2 and carrying out RT-PCR assays. The percentage of Bcl-xS is represented in histograms with asterisks indicating p values when samples are compared to wild-type HA-SRSF10. Error bars indicate SD. *p < 0.05, **p < 0.01, and ***p < 0.001. (F) The anti-F, anti-H, and anti-K immunoprecipitations used extracts from cells expressing RS1-FLAG or RS1-ΔΔ-FLAG (structure diagrammed on top). The procedure is as described in Figure 3E. A rabbit IgG was used in the control immunoprecipitation.

Figure 6. Impact of the Depletion of SRSF10 on the Oxaliplatin-Induced Splicing Shifts

(A) Immunoblot showing the siRNA-mediated depletion of SRSF10 in cells treated or not with oxaliplatin. (B–H) For each subsequent panel, the name of the gene and the structure of its relevant portion are shown. (B) BRCA1. Exon numbers are shown. (C) CHEK2. Size of exons in nucleotides. (D) MLH3. Size of exons in nucleotides. (E) RBBP8. Size of exons in nucleotides. (F) PCBP4. Size of exons in nucleotides. (G) TNFRSF10B. Size of exons in nucleotides. (H) CASP8. Size of exons in nucleotides. In each panel, the RT-PCR analysis presents electrophero-grams with molecular weight markers. Triplicate experiments are shown as histograms with percent splicing index (PSI). Error bars indicate SD. Asterisks indicate significant P values obtained when comparing control with siSRSF10 or samples treated with oxaliplatin with samples treated with both siSRSF10 and oxaliplatin; *p < 0.05, **p < 0.01, and ***p < 0.001.