Germann, S., Gratadou, L., Dutertre, M. & Auboeuf, D. Splicing programs and cancer. J. Nucleic Acids 2012, 269570 (2012).
Kalsotra, A. & Cooper, T. A. Functional consequences of developmentally regulated alternative splicing. Nat. Rev. Genet. 12, 715-729 (2011).
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B. & Tian, B. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. US A 106, 7028-7033 (2009).
Ji, Z. & Tian, B. Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 4, e8419 (2009).
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1647 (2008). (Pubitemid 351931255)
Elkon, R. et al. E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol. 13, R59 (2012).
Elkon, R., Ugalde, A. P. & Agami, R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14, 496-506 (2013).
Di Giammartino, D. C., Nishida, K. & Manley, J. L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866 (2011).
Tian, B., Pan, Z. & Lee, J. Y. Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res. 17, 156-165 (2007). (Pubitemid 46220760)
Vorlova, S. et al. Induction of antagonistic soluble decoy receptor tyrosine kinases by intronic polyA activation. Mol. Cell 43, 927-939 (2011).
Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53-64 (2012).
Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664-668 (2010).
Lee, J. Y., Ji, Z. & Tian, B. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. Nucleic Acids Res. 36, 5581-5590 (2008).
Zhang, H., Lee, J. Y. & Tian, B. Biased alternative polyadenylation in human tissues. Genome Biol. 6, R100 (2005).
Flavell, S. W. et al. Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60, 1022-1038 (2008).
Dutertre, M., Sanchez, G., Barbier, J., Corcos, L. & Auboeuf, D. The emerging role of pre-messenger RNA splicing in stress responses: sending alternative messages and silent messengers. RNA Biol. 8, 740-747 (2011).
Kleiman, F. E. & Manley, J. L. The BARD1-CstF-50 interaction links mRNA 3' end formation to DNA damage and tumor suppression. Cell 104, 743-753 (2001). (Pubitemid 32241024)
Decorsiere, A., Cayrel, A., Vagner, S. & Millevoi, S. Essential role for the interaction between hnRNP H/F and a G quadruplex in maintaining p53 premRNA 3'-end processing and function during DNA damage. Genes Dev. 25, 220-225 (2011).
Munoz, M. J. et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 137, 708-720 (2009).
Solier, S. et al. Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors. Cancer Res. 70, 8055-8065 (2010).
Ip, J. Y. et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 21, 390-401 (2011).
Dutertre, M. et al. Cotranscriptional exon skipping in the genotoxic stress response. Nat. Struct. Mol. Biol. 17, 1358-1366 (2010).
Collins, I., Weber, A. & Levens, D. Transcriptional consequences of topoisomerase inhibition. Mol. Cell Biol. 21, 8437-8451 (2001). (Pubitemid 33108603)
Graber, J. H. et al. DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast. Genome Res. 23, 1690-1703 (2013).
Busa, 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. 38, 3005-3018 (2010).
Solier, S. et al. Topoisomerase I and II inhibitors control caspase-2 premessenger RNA splicing in human cells. Mol. Cancer Res. 2, 53-61 (2004). (Pubitemid 38167108)
Albert, H., Battaglia, E., Monteiro, C. & Bagrel, D. Genotoxic stress modulates CDC25C phosphatase alternative splicing in human breast cancer cell lines. Mol. Oncol. 6, 542-552 (2012).
Kolb, R. H., Greer, P. M., Cao, P. T., Cowan, K. H. & Yan, Y. ERK1/2 signaling plays an important role in topoisomerase II poison-induced G2/M checkpoint activation. PLoS One 7, e50281 (2012).
Foltz, D. R. et al. The human CENP-A centromeric nucleosome-associated complex. Nat. Cell Biol. 8, 458-469 (2006).
Carroll, C. W., Silva, M. C., Godek, K. M., Jansen, L. E. & Straight, A. F. Centromere assembly requires the direct recognition of CENP-A nucleosomes by CENP-N. Nat. Cell Biol. 11, 896-902 (2009).
McClelland, S. E. et al. The CENP-A NAC/CAD kinetochore complex controls chromosome congression and spindle bipolarity. EMBO J. 26, 5033-5047 (2007). (Pubitemid 350261290)
Hellwig, D. et al. Dynamics of CENP-N kinetochore binding during the cell cycle. J. Cell Sci. 124, 3871-3883 (2011).
Nag, A., Narsinh, K. & Martinson, H. G. The poly(A)-dependent transcriptional pause is mediated by CPSF acting on the body of the polymerase. Nat. Struct. Mol. Biol. 14, 662-669 (2007). (Pubitemid 47037062)
Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
Kleiman, F. E. & Manley, J. L. Functional interaction of BRCA1-associated BARD1 with polyadenylation factor CstF-50. Science 285, 1576-1579 (1999). (Pubitemid 29420583)
Gorospe, M. HuR in the mammalian genotoxic response: post-transcriptional multitasking. Cell Cycle 2, 412-414 (2003).
Mukherjee, N. et al. Integrative regulatory mapping indicates that the RNAbinding protein HuR couples pre-mRNA processing and mRNA stability. Mol. Cell 43, 327-339 (2011).
Lebedeva, S. et al. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol. Cell 43, 340-352 (2011).
Izquierdo, J. M. Hu antigen R (HuR) functions as an alternative pre-mRNA splicing regulator of Fas apoptosis-promoting receptor on exon definition. J. Biol. Chem. 283, 19077-19084 (2008).
Zhou, H. L. et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc. Natl Acad. Sci. USA 108, E627-E635 (2011).
Dai, W., Zhang, G. & Makeyev, E. V. RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage. Nucleic Acids Res. 40, 787-800 (2012).
Zhu, H., Zhou, H. L., Hasman, R. A. & Lou, H. Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences. J. Biol. Chem. 282, 2203-2210 (2007). (Pubitemid 47076748)
Latorre, E. et al. Downregulation of HuR as a new mechanism of doxorubicin resistance in breast cancer cells. Mol. Cancer 11, 13 (2012).
Simone, L. E. & Keene, J. D. Mechanisms coordinating ELAV/Hu mRNA regulons. Curr. Opin. Genet. Dev. 23, 35-43 (2013).
Mazan-Mamczarz, K. et al. ATM regulates a DNA damage response posttranscriptional RNA operon in lymphocytes. Blood 117, 2441-2450 (2011).
Kim, H. H., Abdelmohsen, K. & Gorospe, M. Regulation of HuR by DNA Damage Response Kinases. J. Nucleic Acids 2010, 981487 (2010).
Masuda, K. et al. Global dissociation of HuR-mRNA complexes promotes cell survival after ionizing radiation. EMBO. J. 30, 1040-1053 (2011).
Wang, W. et al. HuR regulates p21 mRNA stabilization by UV light. Mol. Cell Biol. 20, 760-769 (2000). (Pubitemid 30044212)
Westmark, C. J., Bartleson, V. B. & Malter, J. S. RhoB mRNA is stabilized by HuR after UV light. Oncogene 24, 502-511 (2005). (Pubitemid 40188597)
Munirajan, A. K. et al. KIF1Bbeta functions as a haploinsufficient tumor suppressor gene mapped to chromosome 1p36.2 by inducing apoptotic cell death. J. Biol. Chem. 283, 24426-24434 (2008).
Xu, J. et al. Silencing of MBD1 reverses pancreatic cancer therapy resistance through inhibition of DNA damage repair. Int. J. Oncol. 42, 2046-2052 (2013).
Moore, M. J., Wang, Q., Kennedy, C. J. & Silver, P. A. An alternative splicing network links cell-cycle control to apoptosis. Cell 142, 625-636 (2010).
Shin, C. & Manley, J. L. The SR protein SRp38 represses splicing in M phase cells. Cell 111, 407-417 (2002). (Pubitemid 35341393)
Porter, A. C. & Farr, C. J. Topoisomerase II: untangling its contribution at the centromere. Chromosome Res. 12, 569-583 (2004). (Pubitemid 41217416)
Weng, M. T. et al. Evolutionarily conserved protein ERH controls CENP-E mRNA splicing and is required for the survival of KRAS mutant cancer cells. Proc. Natl Acad. Sci. USA 109, E3659-E3667 (2012).
Sanchez, G. et al. Alteration of cyclin D1 transcript elongation by a mutated transcription factor up-regulates the oncogenic D1b splice isoform in cancer. Proc. Natl Acad. Sci. USA 105, 6004-6009 (2008). (Pubitemid 351758389)
Paronetto, M. P., Minana, B. & Valcarcel, J. The Ewing sarcoma protein regulates DNA damage-induced alternative splicing. Mol. Cell 43, 353-368 (2011).
Zeitlin, S. G. et al. Double-strand DNA breaks recruit the centromeric histone CENP-A. Proc. Natl Acad. Sci. USA 106, 15762-15767 (2009).
Liu, S. T., Rattner, J. B., Jablonski, S. A. & Yen, T. J. Mapping the assembly pathways that specify formation of the trilaminar kinetochore plates in human cells. J. Cell Biol. 175, 41-53 (2006). (Pubitemid 44537197)
Mallinjoud, P. et al. Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin. Genome Res. doi:10.1101/gr.162933.113 (2013).
Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
Huang da, W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715 (2004). (Pubitemid 38500244)
