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. 2010 Jul 1;7(4):390–396. doi: 10.4161/rna.7.4.12466

An emerging role for nuclear RNA-mediated responses to genotoxic stress

Roberta Busà 1, Claudio Sette 1,✉
PMCID: PMC3070907  PMID: 20639695

Abstract

Defects in the regulation of alternative splicing have strong relevance in the onset and progression of several types of human cancer. Modulation of alternative splicing allows cancer cells to adapt to hostile environments through production of specific mRNA variants. In particular, genotoxic stress exerted by chemotherapeutic drugs or irradiation strongly affects splicing of many genes. A key role in this aberrant regulation is played by the unbalanced expression of several splicing factors in cancer cells. Among them, the RNA-binding protein Sam68, which is overexpressed in various tumors, was shown to accumulate in nuclear foci of active transcription, together with other splicing regulators, and to affect splicing of target mRNAs in response to genotoxic stress. We suggest that subcellular redistribution of splicing factors is guided by changes in chromatin conformation elicited by DNA-damaging drugs. This event might represent an escape mechanism used by cancer cells to survive to genotoxic insults through expression of pro-survival, cancer-specific gene products.

Key words: genotoxic stress, nuclear stress granules, alternative splicing, chromatin structure, Sam68

Alternative Splicing and Cancer

Alternative splicing (AS) has recently emerged as an important contributor to biological diversity in higher eukaryotes. Transcriptome analyses have revealed that most multi-exon human genes encode for at least two isoforms through differential assortment of exonic sequences in the mature mRNA.1,2 AS has been proposed to underlie the immense complexity observed in the mammalian proteome in spite of the relatively limited number of genes.3 In line with its envisioned contribution to cellular diversity, AS-regulated gene expression guides many different processes, such as apoptosis, sex determination, axon guidance, cell excitation and contraction.4–7 On the other hand, aberrant regulation of AS is associated with various human diseases.8,9 In particular, the crucial contribution of AS to neoplastic transformation is well described. Aberrant splicing events characterize many types of cancer, like prostate,10,11 breast12 and ovarian carcinomas.13,14 Since these cancer-specific events often correlate with the stage of disease, they represent a “splicing signature” that characterizes tumor subgroups, thereby providing prognostic value and offering potential cancer-specific targets for therapeutic approaches.15

The mechanisms causing AS deregulation in cancer begin to be understood. Several disease-associated mutations were shown to affect splicing of oncogenes, tumour suppressors and other cancer relevant genes, involved in apoptosis, cell invasion and angiogenesis.16,17 The mRNA variants yielded by these cancer-specific AS events often provide an advantage in terms of cell proliferation and/or survival. However, examples also exists of aberrantly spliced isoforms found in the absence of mutations in the affected genes.16,17 Possibly, alterations in the splicing machinery of cancer cells, due to unbalanced expression of spliceosomal components and/or splicing regulators,18,19 underlie such aberrant AS events. More ground to this hypothesis was provided by the demonstration that overexpression of a single splicing factor, the SR protein ASF/SF2, can trigger malignant transformation.20 ASF/SF2 is upregulated in various human tumors, partly because of gene amplification. This altered regulation of ASF/SF2 expression leads to production of new splicing variants from a subset of genes, which encode proteins displaying oncogenic properties that might support malignant transformation.20 Additional splicing factors are upregulated in some types of cancer and promote AS of isoforms with strong relevance to tumour cell biology.15 For instance, the hnRNPs A1, A2 and I (polypyrimidine tract-binding protein, PTB) have been recently shown to enhance splicing of the pyruvate kinase isoform PKM2,21,22 which endows cancer cells with higher metabolic rate.23 Loss of function of a splicing factor might also result in cancer. RBM5 is downregulated in 60–70% of lung cancers,24 likely because the gene encoding this protein (RBM5/LUCA-15/H37) is often deleted in human lung cancer.25 RBM5 modulates AS of genes involved in cell death, such as CASP226 and FAS,27 and deletion of this tumor suppressor protein in cancer might promote cell survival. Similarly, down-regulation of the splicing regulator FOX2 seems to be responsible for a large percentage of the aberrant AS events observed in ovarian and breast cancer cells.14

Our laboratory has recently identified the RNA-binding protein (RBP) Sam68 as an important regulator of AS events in prostate cancer (PCa). Sam68 is frequently upregulated in PCa,28,29 in renal carcinoma30 and in other types of cancer, such as liver and thyroid cancers (Fig. 1). Moreover, depletion of Sam68 by RNAi reduced PCa cell proliferation,28 whereas genetic haploinsufficiency of Sam68 delayed the onset of mammary tumors and reduced the number of metastases in an animal model of breast cancer.31 These results have unveiled a novel role for Sam68 in tumor cell biology and suggested that interfering with its function might impair cancer cell proliferation and survival.32

Figure 1.

Figure 1

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Sam68 is upregulated in liver and thyroid tumors. Sam68 expression was analyzed by immunohistochemistry in human liver and thyroid cancer specimens. (A–C) Specimen of liver tumor. (A) Neoplastic lesion and surrounding normal tissue. (B and C) Higher magnification of neoplastic and normal tissue, respectively. (D–F) Specimen of thyroid tumor. (D) Neoplastic lesion and surrounding normal follicular structure. (E and F) Higher magnification of neoplastic and normal tissues, respectively.

Sam68: A Multifunctional RNA-Binding Protein Involved in RNA Processing

Sam68 is implicated in several steps of mRNA processing. In the cytoplasm, it enhances translation of viral and cellular mRNAs through association with the translation initiation complex eIF4F and the polyribosomes.33–36 In the nucleus, Sam68 integrates signal transduction pathways with AS in response to extra- cellular cues.37–39 The first Sam68 mRNA target identified was CD44,37 a membrane receptor aberrantly expressed in neoplastic tissues.40 Sam68 mediates inclusion of the CD44 variable exons v5,37 and v6,41 under the influence of the RAS/ERK pathway.37,42 Our laboratory has identified two additional Sam68 mRNA targets with strong relevance to PCa: Bcl-x38 and Cyclin D1.39 Bcl-x encodes for a long antiapoptotic isoform, Bcl-x(L), and a short proapoptotic isoform, Bcl-x(s). Upregulation of Sam68 normally promotes splicing of Bcl-x(s) and apoptosis.38 However, Sam68 is often phosphorylated in tyrosine residues in cancer cells,43,44 and this modification may promote splicing of Bcl-x(L) and cell survival.38 The Cyclin D1 mRNA is alternatively spliced to give two isoforms: D1a, the most abundant form, and D1b, associated with increased PCa risk.45,46 We recently demonstrated that Sam68 binds to Cyclin D1 mRNA and favours splicing of the D1b variant.39 Since this isoform promotes growth of PCa cells45 and was suggested to confer resistance to therapeutic treatment of breast cancer cells,47 it is likely that splicing of Cyclin D1b is part of the protective role exerted by Sam68 in PCa cells.28

Genotoxic Stress and Changes in Alternative Splicing

Mounting evidence is pointing to an important role of AS in the cellular response to genotoxic stress. Changes in splicing variants have been observed in cancer cells treated with cisplatin or etoposide.47–51 Remarkably, these drugs affect splicing of genes encoding for proteins that regulate apoptosis (Caspase 2 and Bcl-2 related genes)48,49 cell motility (CD44)50 and proliferation (Cyclin D1b, MDM2 and MDM4).47,51 A more global analysis using exon-junction microarrays revealed a large spectrum of changes in AS after irradiation with ultraviolet light (UV).49 Interestingly, AS events can vary depending on the cancer cell type and/or the genotoxic drug used,52 suggesting that AS is differently tuned depending on the cell context and that its regulation cannot be easily predicted. Much less is known on the mechanisms activated during genotoxic stress that result in the observed splicing changes. It has been proposed that AS events in response to UV irradiation are guided by phosphorylation of the RNA polymerase II (RNAPII) and consequent modification of the rate of transcription.49 However, many genes undergoing AS changes in response to stimuli are not affected at the gene expression level,53 suggesting that additional mechanisms are likely involved.

An RNA-Mediated Cellular Response to Stress

DNA damage causes subcellular redistribution of many RBPs, suggesting that this response is an attempt of the cell to survive in the hostile environment. Double strand breaks induced by cisplatin determine accumulation of RDM1, an RNA recognition motif (RRM)-containing protein, in the nucleolus, thus sequestering it from the nucleoplasm.54 UV irradiation triggers cytoplasmic translocation of hnRNP A1,55 and it was suggested that its export from the nucleus would affect AS events regulated by this splicing factor.56 However, UV doses (10–50 J/m2) lower than those required to affect hnRNP A1 localization are sufficient to elicit a splicing response.49,55 Similarly, cisplatintreatment can alter AS profile of specific mRNAs without affecting the subcellular localization of splicing factors belonging to the SR family.49 Thus, mild DNA insults appear to mainly affect AS through modulation of the phosphorylation status of RNAPII,49 likely by decreasing the transcription rate and favoring usage of weak splice sites.49,57,58 On the other hand, changes in localization of splicing factors occurring after stronger genotoxic insults might be responsible for additional DNA damage-induced splicing events.54–56

UV light, heat shock, chemical and hyper-osmotic stresses, can induce accumulation of several RBPs in nuclear stress bodies (nSBs).56,59–61 These granules, which transiently appear in the stressed cell, are assembled in chromatin regions composed of long tandem arrays of Satellite III (SatIII) DNA that are transcribed into non-coding RNAs.61 SatIII RNAs remain bound to sites of transcription and recruit SAF-B, ASF/SF2 and Sam68 to form the nSBs.60 Although SatIII RNAs were proposed to titer out splicing factors and to influence indirectly splicing events, the function of these non-coding RNAs is not fully understood yet.56

Since expression of Sam68 elicits a protective effect in PCa cells exposed to genotoxic stress,28 we have investigated whether its subcellular localization was affected by treatment with mitoxantrone (MTX), a topoisomerase II inhibitor used in chemotherapy. MTX induced relocalization of Sam68 into nuclear granules, together with several other RBPs involved in AS and other steps of post-transcriptional regulation of mRNAs, like hnRNP A1 and TIA-1 and the SR proteins SC35 and ASF/SF2.62 Since the repertoire of RBPs recruited to MTX-induced nuclear granules partially differed from that reported for nSBs, they are probably different structures. Indeed, MTX did not induce SatIII transcription, suggesting that these nuclear granules are involved in other aspects of the cellular response to genotoxic stress. Further characterization of the MTX-induced granules indicated that they are transcriptionally active foci of chromatin (BrU-positive, see Fig. 2), and that they also accumulate the phosphorylated form of RNAPII,62 which is normally engaged in transcript elongation.63

Figure 2.

Figure 2

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Genotoxic stress-induced Sam68 nuclear granules are transcriptionally active. BrU staining of PC3 cells treated for 24 h with 5 µM MTX. Cells were also stained for Sam68 as previously described.60 Confocal microscopy analysis showed that Sam68 nuclear granules are BrU-positive foci of active transcription. Scale bar = 10 µm

Thus, MTX-induced nuclear granules display features of active structures involved in de novo transcription and processing of transcripts in cells exposed to genotoxic stress.

A Role for Nuclear Granules as Drug-Induced “Splicing Factories?”

The observation that DNA damage induced relocalization of splicing factors into foci of residual transcription suggested that this response process might regulate pre-mRNA AS. Thus, we investigated whether changes in subcellular localization of Sam68 induced by MTX affected AS of its target CD44. We chose CD44 because its AS was previously shown to undergo regulation during genotoxic stress.50 MTX enhanced inclusion of the Sam68-target exon v5, both in the endogenous mRNA and in a reporter minigene. This splicing event was dependent on Sam68 expression, as it was repressed by RNAi depletion of the endogenous protein and recovered by transfection of a non-degradable recombinant Sam68 transcript.62 Notably, inclusion of variable exons in the CD44 pre-mRNA results in expression of oncogenic forms of the receptor that support proliferation, invasiveness and survival of cancer cells.64 Thus, we hypothesize that accumulation of Sam68, and of other splicing factors, into transcriptionally active granules alters the cellular AS pattern and might represent a way for the cells to cope with lesions elicited by genotoxic insults (Fig. 3).

Figure 3.

Figure 3

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Hypothetical model of genotoxic stress-induced changes in alternative splicing elicited by accumulation of a splicing factor in transcriptionally active nuclear foci. (A) In untreated cells Sam68 and RNA polymerase II (RNAPII) are diffused in the nucleoplasm. (B) Following genotoxic stress, Sam68 accumulates into nuclear granules of active transcription colocalizing with the phosphorylated form of RNAPII. The increased concentration of Sam68 on specific nascent pre-mRNAs (i.e., CD44) could lead to changes in AS, like in the case of exon v5 inclusion. Thus, relocalization of Sam68 and other RBPs into foci of residual transcription could modulate AS of a specific set of pre-mRNAs and confer drug resistance to cancer cells, promoting their survival from genotoxic stress.

The accumulation of splicing factors in nuclear granules could be due to post-translational modification of these proteins. A similar regulation was demonstrated for the stress-induced translocation of hnRNP A1 in the cytoplasm and its accumulation in stress granules (SGs).55 Cytoplasmic SGs are structures involved in translational repression and storage of mRNAs upon stress and they are characterized by the presence of TIA-1 and hnRNP A1.65 Since we observed that MTX also caused accumulation of Sam68 in cytoplasmic SGs in a small percentage of cells, we asked whether post-translational modification of Sam68 was involved in its accumulation in nuclear and cytoplasmic stress granules. We found that MTX induces activation of the ATM/Chk2, JNK, p38 and ERK1/2 pathways. However, inhibition of all these pathways did not affect Sam68 recruitment to stress granules, nor that of hnRNP A1 and TIA-1, suggesting that a different mechanism is responsible for accumulation of these splicing factors at sites of active transcription.62

An Epigenetic Code for the RNA-Mediated Genotoxic Response?

Another possibility is that genotoxic stress affects chromatin structure, thereby exposing domains that are more accessible to the transcription and splicing machineries. Indeed, biochemical fractionation of chromatin supported this hypothesis, and we found differential enrichment of Sam68 and hnRNP A1 in specific chromatin fractions after MTX treatment.62 However, how genotoxic stress renders these chromatin domains more receptive of RBPs involved in transcription and splicing remains unknown. An intriguing possibility is that epigenetic modifications of the chromatin underlie such effect. It is well known that DNA damage induces epigenetic modifications of histones,66 the most characterized of which being ATM-mediated phosphorylation of H2AX.67 Support to this hypothesis is provided by a recent report showing that genotoxic stress caused by camptothecin, a topoisomerase I inhibitor, enhanced chromatin acetylation and altered splicing of the HIF1A locus in cancer cells.68 Moreover, a direct role for histone modifications in AS regulation has been recently proposed. Epigenetic signatures correlated with specific splicing events in human differentiated and stem cells, and changes in histone modifications directly affected AS through recruitment of PTB.69 The mechanism involved the direct interaction of this splicing regulator with a chromatin-binding protein (MRG15), and it is likely that more examples in this sense will soon be described.

Conclusions: A Model for Nuclear RNA-Mediated Stress Response

Cancer cells have developed different ways to withstand genotoxic stresses affecting the integrity of the genome, like irradiation or exposure to alkylating agents, gaining resistance to chemotherapeutic treatments. Depending on the nature and the intensity of the genotoxic stress, cells trigger different signaling pathways to set in motion multiple mechanisms to deal with adducts, mismatches or double strand breaks to preserve genomic stability and promote survival.70

Herein, we have discussed the role played by changes in localization of splicing factors, and consequent modification of AS, in response to genotoxic stress induced by MTX. This mechanism involves several RBPs and will likely affect a large spectrum of AS events. We propose that, in addition to changes in the rate of transcription,49 genotoxic stress may alter AS regulation through changes in chromatin structure, thereby favouring the recruitment of a set of splicing factors to transcriptionally active nuclear foci. An attractive hypothesis is that stress-induced epigenetic modifications within specific loci attract splicing factors to distinct exons or introns. This redistribution of RBPs inside the nucleus may be required to promote splicing of mRNA variants encoding proteins that confer a survival advantage to the cell. In particular, we have focused our attention on Sam68, a multifunctional RBP that acts as scaffold in signal transduction pathways and links them to RNA processing events.71,72 For its features, Sam68 represents a prototype of RBPs involved in the response to external cues, and its involvement in cellular adaptation to many stresses has been documented. In addition to the newly described regulation during genotoxic stress,62 it was shown that in cells infected with poliovirus, Sam68 accumulates in cytoplasmic SGs, containing both host mRNAs and TIA-1.73 In the cytoplasm, Sam68 interacts with poliovirus RNA polymerase and may support poliovirus replication.74 Similarly, Sam68 enhances HIV infection by favouring nuclear export75 and utilization of viral RNAs.33 This role is essential, because Sam68-depleted cells are resistant to HIV infection,76 whereas expression of a truncated Sam68 mutant impairs infection by sequestering viral nef mRNA into SGs.77 Lastly, bortezomib, a proteasome inhibitor used in chemotherapy, induces accumulation of Sam68, poly(A)-binding protein 1 and poly(A)-RNAs in transcription-free nuclear granules, which could function as transient mRNA storage and stabilization sites that eventually allow cell recovery after the stress ceases.78

In conclusion, we suggest a new role for Sam68 and other splicing factors in the RNA-mediated cellular stress response, in which these RBPs could take an active part by changing subcellular localization. Thus, elucidation of their function in response to genotoxic stress might reveal general concepts involved in adaptation of cancer cells to external cues that cause genomic instability, and provide examples of how RNA-binding proteins participate to this response through changes in the RNA repertoire of the cell.

Acknowledgements

The authors wish to thank Drs. Maria Paola Paronetto, Simona Pedrotti, Claudia Compagnucci for their helpful suggestions and discussion. Work in the laboratory of Claudio Sette was supported by Grants from the “Associazione Italiana Ricerca sul Cancro” (AIRC), the “Association for International Cancer Research” (AICR) and Telethon.

Footnotes

References

  • 1.Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456:470–476. doi: 10.1038/nature07509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40:1413–1415. doi: 10.1038/ng.259. [DOI] [PubMed] [Google Scholar]
  • 3.Hartmann B, Valcárcel J. Decrypting the genome's alternative messages. Curr Opin Cell Biol. 2009;21:377–386. doi: 10.1016/j.ceb.2009.02.006. [DOI] [PubMed] [Google Scholar]
  • 4.Maniatis T, Tasic B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature. 2002;418:236–243. doi: 10.1038/418236a. [DOI] [PubMed] [Google Scholar]
  • 5.Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003;72:291–336. doi: 10.1146/annurev.biochem.72.121801.161720. [DOI] [PubMed] [Google Scholar]
  • 6.Li Q, Lee JA, Black DL. Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci. 2007;8:819–831. doi: 10.1038/nrn2237. [DOI] [PubMed] [Google Scholar]
  • 7.Chen M, Manley JL. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol. 2009;10:741–754. doi: 10.1038/nrm2777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet. 2007;8:749–761. doi: 10.1038/nrg2164. [DOI] [PubMed] [Google Scholar]
  • 9.Tazi J, Bakkour N, Stamm S. Alternative splicing and disease. Biochim Biophys Acta. 2009;1792:14–26. doi: 10.1016/j.bbadis.2008.09.017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Li HR, Wang-Rodriguez J, Nair TM, Yeakley JM, Kwon YS, Bibikova M, et al. Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res. 2006;66:4079–4088. doi: 10.1158/0008-5472.CAN-05-4264. [DOI] [PubMed] [Google Scholar]
  • 11.Zhang C, Li HR, Fan JB, Wang-Rodriguez J, Downs T, Fu XD, et al. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics. 2006;7:202–213. doi: 10.1186/1471-2105-7-202. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, et al. Identification of alternative splicing markers for breast cancer. Cancer Res. 2008;68:9525–9531. doi: 10.1158/0008-5472.CAN-08-1769. [DOI] [PubMed] [Google Scholar]
  • 13.Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Gervais-Bird J, Madden R, et al. Multiple alternative splicing markers for ovarian cancer. Cancer Res. 2008;68:657–663. doi: 10.1158/0008-5472.CAN-07-2580. [DOI] [PubMed] [Google Scholar]
  • 14.Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, et al. Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol. 2009;16:670–676. doi: 10.1038/nsmb.1608. [DOI] [PubMed] [Google Scholar]
  • 15.Grosso AR, Martins S, Carmo-Fonseca M. The emerging role of splicing factors in cancer. EMBO Rep. 2008;9:1087–1093. doi: 10.1038/embor.2008.189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Venables JP. Unbalanced alternative splicing and its significance in cancer. Bioessays. 2006;28:378–386. doi: 10.1002/bies.20390. [DOI] [PubMed] [Google Scholar]
  • 17.Ghigna C, Valacca C, Biamonti G. Alternative splicing and tumor progression. Curr Genomics. 2008;9:556–570. doi: 10.2174/138920208786847971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Kim E, Goren A, Ast G. Insights into the connection between cancer and alternative splicing. Trends Genet. 2008;24:7–10. doi: 10.1016/j.tig.2007.10.001. [DOI] [PubMed] [Google Scholar]
  • 19.Ritchie W, Granjeaud S, Puthier D, Gautheret D. Entropy measures quantify global splicing disorders in cancer. PLoS Comput Biol. 2008;4:1000011. doi: 10.1371/journal.pcbi.1000011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Karni R, de Stanchina E, Lowe SW, Sinha R, Mu D, Krainer AR. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol. 2007;14:185–193. doi: 10.1038/nsmb1209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.David CJ, Chen M, Assanah M, Canoll P, Manley JL. HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer. Nature. 2010;463:364–368. doi: 10.1038/nature08697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Clower CV, Chatterjee D, Wang Z, Cantley LC, Vander Heiden MG, Krainer AR. The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proc Natl Acad Sci USA. 2010;107:1894–1899. doi: 10.1073/pnas.0914845107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Christofk HR, Vander Heiden MG, Harris MH, Ramanathan A, Gerszten RE, Wei R, et al. The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour growth. Nature. 2008;452:230–233. doi: 10.1038/nature06734. [DOI] [PubMed] [Google Scholar]
  • 24.Oh JJ, West AR, Fishbein MC, Slamon DJ. A candidate tumor suppressor gene, H37, from the human lung cancer tumor suppressor locus 3p21.3. Cancer Res. 2002;62:3207–3213. [PubMed] [Google Scholar]
  • 25.Lerman MI, Minna JD. The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium. Cancer Res. 2000;60:6116–6133. [PubMed] [Google Scholar]
  • 26.Fushimi K, Ray P, Kar A, Wang L, Sutherland LC, Wu JY. Upregulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM5. Proc Natl Acad Sci USA. 2008;105:15708–15713. doi: 10.1073/pnas.0805569105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Bonnal S, Martínez C, Förch P, Bachi A, Wilm M, Valcárcel J. RBM5/Luca-15/H37 regulates Fas alternative splice site pairing after exon definition. Mol Cell. 2008;32:81–95. doi: 10.1016/j.molcel.2008.08.008. [DOI] [PubMed] [Google Scholar]
  • 28.Busà R, Paronetto MP, Farini D, Pierantozzi E, Botti F, Angelini DF, et al. The RNA-binding protein Sam68 contributes to proliferation and survival of human prostate cancer cells. Oncogene. 2007;26:4372–4382. doi: 10.1038/sj.onc.1210224. [DOI] [PubMed] [Google Scholar]
  • 29.Rajan P, Gaughan L, Dalgliesh C, El-Sherif A, Robson CN, Leung HY, et al. The RNA-binding and adaptor protein Sam68 modulates signal-dependent splicing and transcriptional activity of the androgen receptor. J Pathol. 200;215:67–77. doi: 10.1002/path.2324. [DOI] [PubMed] [Google Scholar]
  • 30.Zhang Z, Li J, Zheng H, Yu C, Chen J, Liu Z, et al. Expression and cytoplasmic localization of SAM68 is a significant and independent prognostic marker for renal cell carcinoma. Cancer Epidemiol Biomarkers Prev. 2009;18:2685–2693. doi: 10.1158/1055-9965.EPI-09-0097. [DOI] [PubMed] [Google Scholar]
  • 31.Richard S, Vogel G, Huot ME, Guo T, Muller WJ, Lukong KE. Sam68 haploinsufficiency delays onset of mammary tumorigenesis and metastasis. Oncogene. 2008;27:548–556. doi: 10.1038/sj.onc.1210652. [DOI] [PubMed] [Google Scholar]
  • 32.Lukong KE, Richard S. Targeting the RNA-binding protein Sam68 as a treatment for cancer? Future Oncol. 2007;3:539–544. doi: 10.2217/14796694.3.5.539. [DOI] [PubMed] [Google Scholar]
  • 33.Coyle JH, Guzik BW, Bor YC, Jin L, Eisner-Smerage L, Taylor SJ, et al. Sam68 enhances the cytoplasmic utilization of intron-containing RNA and is functionally regulated by the nuclear kinase Sik/BRK. Mol Cell Biol. 2003;23:92–103. doi: 10.1128/MCB.23.1.92-103.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Paronetto MP, Zalfa F, Botti F, Geremia R, Bagni C, Sette C. The nuclear RNA-binding protein Sam68 translocates to the cytoplasm and associates with the polysomes in mouse spermatocytes. Mol Biol Cell. 2006;17:14–24. doi: 10.1091/mbc.E05-06-0548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Paronetto MP, Messina V, Bianchi E, Barchi M, Vogel G, Moretti C, et al. Sam68 regulates translation of target mRNAs in male germ cells, necessary for mouse spermatogenesis. J Cell Biol. 2009;185:235–249. doi: 10.1083/jcb.200811138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Grange J, Belly A, Dupas S, Trembleau A, Sadoul R, Goldberg Y. Specific interaction between Sam68 and neuronal mRNAs: implication for the activity-dependent biosynthesis of elongation factor eEF1A. J Neurosci Res. 2009;87:12–25. doi: 10.1002/jnr.21824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Matter N, Herrlich P, Konig H. Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature. 2002;420:691–695. doi: 10.1038/nature01153. [DOI] [PubMed] [Google Scholar]
  • 38.Paronetto MP, Achsel T, Massiello A, Chalfant CE, Sette C. The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x. J Cell Biol. 2007;176:929–939. doi: 10.1083/jcb.200701005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Paronetto MP, Cappellari M, Busà R, Pedrotti S, Vitali R, Comstock C, et al. Alternative splicing of the cyclin D1 proto-oncogene is regulated by the RNA-binding protein Sam68. Cancer Res. 2010;70:229–239. doi: 10.1158/0008-5472.CAN-09-2788. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Naor D, Sionov RV, Ish-Shalom D. CD44: structure, function and association with the malignant process. Adv Cancer Res. 1997;71:241–319. doi: 10.1016/s0065-230x(08)60101-3. [DOI] [PubMed] [Google Scholar]
  • 41.Cheng C, Sharp PA. Regulation of CD44 alternative splicing by SRm160 and its potential role in tumor cell invasion. Mol Cell Biol. 2006;26:362–370. doi: 10.1128/MCB.26.1.362-370.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Batsché E, Ianiv M, Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol. 2006;13:22–29. doi: 10.1038/nsmb1030. [DOI] [PubMed] [Google Scholar]
  • 43.Paronetto MP, Farini D, Sammarco I, Maturo G, Vespasiani G, Geremia R, et al. Expression of a truncated form of the c-Kit tyrosine kinase receptor and activation of Src kinase in human prostatic cancer. Am J Pathol. 2004;164:1243–1251. doi: 10.1016/S0002-9440(10)63212-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 44.Lukong KE, Larocque D, Tyner AL, Richard S. Tyrosine phosphorylation of sam68 by breast tumor kinase regulates intranuclear localization and cell cycle progression. J Biol Chem. 2005;280:38639–38647. doi: 10.1074/jbc.M505802200. [DOI] [PubMed] [Google Scholar]
  • 45.Burd CJ, Petre CE, Morey LM, Wang Y, Revelo MP, Haiman CA, et al. Cyclin D1b variant influences prostate cancer growth through aberrant androgen receptor regulation. Proc Natl Acad Sci USA. 2006;103:2190–2195. doi: 10.1073/pnas.0506281103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Comstock CE, Augello MA, Benito RP, Karch J, Tran TH, Utama FE, et al. Cyclin D1 splice variants: polymorphism, risk and isoform-specific regulation in prostate cancer. Clin Cancer Res. 2009;15:5338–5349. doi: 10.1158/1078-0432.CCR-08-2865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Wang Y, Dean JL, Millar EK, Tran TH, McNeil CM, Burd CJ, et al. Cyclin D1b is aberrantly regulated in response to therapeutic challenge and promotes resistance to estrogen antagonists. Cancer Res. 2008;68:5628–5638. doi: 10.1158/0008-5472.CAN-07-3170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Solier S, Lansiaux A, Logette E, Wu J, Soret J, Tazi J, et al. Topoisomerase I and II inhibitors control caspase-2 pre-messenger RNA splicing in human cells. Mol Cancer Res. 2004;2:53–61. [PubMed] [Google Scholar]
  • 49.Muñoz MJ, Pérez Santangelo MS, Paronetto MP, de la Mata M, Pelisch F, Boireau S, et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell. 2009;137:708–720. doi: 10.1016/j.cell.2009.03.010. [DOI] [PubMed] [Google Scholar]
  • 50.Filippov V, Filippova M, Duerksen-Hughes PJ. The early response to DNA damage can lead to activation of alternative splicing activity resulting in CD44 splice pattern changes. Cancer Res. 2007;67:7621–7630. doi: 10.1158/0008-5472.CAN-07-0145. [DOI] [PubMed] [Google Scholar]
  • 51.Chandler DS, Singh RK, Caldwell LC, Bitler JL, Lozano G. Genotoxic stress induces coordinately regulated alternative splicing of the p53 modulators MDM2 and MDM4. Cancer Res. 2006;66:9502–9508. doi: 10.1158/0008-5472.CAN-05-4271. [DOI] [PubMed] [Google Scholar]
  • 52.Shkreta L, Froehlich U, Paquet ER, Toutant J, Elela SA, Chabot B. Anticancer drugs affect the alternative splicing of Bcl-x and other human apoptotic genes. Mol Cancer Ther. 2008;7:1398–1409. doi: 10.1158/1535-7163.MCT-08-0192. [DOI] [PubMed] [Google Scholar]
  • 53.Hartmann B, Castelo R, Blanchette M, Boue S, Rio DC, Valcárcel J. Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells. Genome Biol. 2009;10:11. doi: 10.1186/gb-2009-10-1-r11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Messaoudi L, Yang YG, Kinomura A, Stavreva DA, Yan G, Bortolin-Cavaillé ML, et al. Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress. Nucleic Acids Res. 2007;35:6571–6587. doi: 10.1093/nar/gkm753. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 55.Guil S, Long JC, Cáceres JF. hnRNP A1 relocalization to the stress granules reflects a role in the stress response. Mol Cell Biol. 2006;26:5744–5758. doi: 10.1128/MCB.00224-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 56.Biamonti G, Cáceres JF. Cellular stress and RNA splicing. Trends Biochem Sci. 2009;34:146–153. doi: 10.1016/j.tibs.2008.11.004. [DOI] [PubMed] [Google Scholar]
  • 57.Rockx DA, Mason R, van Hoffen A, Barton MC, Citterio E, Bregman DB, et al. UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II. Proc Natl Acad Sci USA. 2000;97:10503–10508. doi: 10.1073/pnas.180169797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 58.de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell. 2003;12:525–532. doi: 10.1016/j.molcel.2003.08.001. [DOI] [PubMed] [Google Scholar]
  • 59.Valgardsdottir R, Chiodi I, Giordano M, Rossi A, Bazzini S, Ghigna C, et al. Transcription of Satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res. 2008;36:423–434. doi: 10.1093/nar/gkm1056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Biamonti G. Nuclear stress bodies: a heterochromatin affair? Nat Rev Mol Cell Biol. 2004;6:93–98. doi: 10.1038/nrm1405. [DOI] [PubMed] [Google Scholar]
  • 61.Valgardsdottir R, Chiodi I, Giordano M, Cobianchi F, Riva S, Biamonti G. Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol Biol Cell. 2005;16:2597–2604. doi: 10.1091/mbc.E04-12-1078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 62.Busà R, Geremia R, Sette C. Genotoxic stress causes the accumulation of the splicing regulator Sam68 in nuclear foci of transcriptionally active chromatin. Nucleic Acids Res. 2010;38:3005–3010. doi: 10.1093/nar/gkq004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 63.Phatnani HP, Greenleaf AL. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 2006;20:2922–2936. doi: 10.1101/gad.1477006. [DOI] [PubMed] [Google Scholar]
  • 64.Ponta H, Sherman L, Herrlich PA. CD44: from adhesion molecules to signalling regulators. Nat Rev Mol Cell Biol. 2003;4:33–45. doi: 10.1038/nrm1004. [DOI] [PubMed] [Google Scholar]
  • 65.Anderson P, Kedersha N. Stress granules: the Tao of RNA triage. Trends Biochem Sci. 2008;33:141–150. doi: 10.1016/j.tibs.2007.12.003. [DOI] [PubMed] [Google Scholar]
  • 66.Zhu Q, Wani AA. Histone modifications: crucial elements for damage response and chromatin restoration. J Cell Physiol. 2010;223:283–288. doi: 10.1002/jcp.22060. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 67.Burma S, Chen BP, Murphy M, Kurimasa A, Chen DJ. ATM phosphorylates histone H2AX in response to DNA double-strand breaks. J Biol Chem. 2001;276:42462–42467. doi: 10.1074/jbc.C100466200. [DOI] [PubMed] [Google Scholar]
  • 68.Baranello L, Bertozzi D, Fogli MV, Pommier Y, Capranico G. DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1alpha gene locus. Nucleic Acids Res. 2010;38:159–171. doi: 10.1093/nar/gkp817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 69.Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science. 2010;327:996–1000. doi: 10.1126/science.1184208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 70.Skorski T. BCR/ABL regulates response to DNA damage: the role in resistance to genotoxic treatment and in genomic instability. Oncogene. 2002;21:8591–8604. doi: 10.1038/sj.onc.1206087. [DOI] [PubMed] [Google Scholar]
  • 71.Lukong KE, Richard S. Sam68, the KH domain-containing superSTAR. Bioch Biophys Acta. 2003;1653:73–86. doi: 10.1016/j.bbcan.2003.09.001. [DOI] [PubMed] [Google Scholar]
  • 72.Sette C, Messina V, Paronetto MP. Sam68: A New STAR in the Male Fertility Firmament. J Androl. 2010;31:66–74. doi: 10.2164/jandrol.109.008136. [DOI] [PubMed] [Google Scholar]
  • 73.Piotrowska J, Hansen SJ, Park N, Jamka K, Sarnow P, Gustin KE. Stable Formation of Compositionally Unique Stress Granules in Virus-infected Cells. J Virol. 2010;84:3654–3665. doi: 10.1128/JVI.01320-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 74.McBride AE, Schlegel A, Kirkegaard K. Human protein Sam68 relocalization and interaction with poliovirus RNA polymerase in infected cells. Proc Natl Acad Sci USA. 1996;93:2296–2301. doi: 10.1073/pnas.93.6.2296. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 75.Reddy TR, Xu W, Mau JK, Goodwin CD, Suhasini M, Tang H, et al. Inhibition of HIV replication by dominant negative mutants of Sam68, a functional homolog of HIV-1 Rev. Nat Med. 1999;5:635–642. doi: 10.1038/9479. [DOI] [PubMed] [Google Scholar]
  • 76.Modem S, Badri KR, Holland TC, Reddy TR. Sam68 is absolutely required for Rev function and HIV-1 production. Nucleic Acids Res. 2005;33:873–879. doi: 10.1093/nar/gki231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 77.Henao-Mejia J, Liu Y, Park IW, Zhang J, Sanford J, He JJ. Suppression of HIV-1 Nef translation by Sam68 mutant-induced stress granules and nef mRNA sequestration. Mol Cell. 2009;33:87–96. doi: 10.1016/j.molcel.2008.11.024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 78.Casafont I, Berciano MT, Lafarga M. Bortezomib induces the formation of nuclear poly(A) RNA granules enriched in Sam68 and PABPN1 in sensory ganglia neurons. Neurotox Res. 2010;17:167–178. doi: 10.1007/s12640-009-9086-1. [DOI] [PubMed] [Google Scholar]

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