An extensive program of periodic alternative splicing linked to cell cycle progression

Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control. DOI: http://dx.doi.org/10.7554/eLife.10288.001

[1]  P. Kaldis,et al.  Mammalian cell-cycle regulation: several Cdks, numerous cyclins and diverse compensatory mechanisms , 2009, Oncogene.

[2]  K. Vermeulen,et al.  The cell cycle: a review of regulation, deregulation and therapeutic targets in cancer , 2003, Cell proliferation.

[3]  T. Pawson,et al.  A mammalian protein kinase with potential for serine/threonine and tyrosine phosphorylation is related to cell cycle regulators. , 1991, The EMBO journal.

[4]  K. Gould,et al.  Myb-Related Fission Yeast cdc5p Is a Component of a 40S snRNP-Containing Complex and Is Essential for Pre-mRNA Splicing , 1999, Molecular and Cellular Biology.

[5]  M. Rapé,et al.  Emerging regulatory mechanisms in ubiquitin-dependent cell cycle control , 2012, Journal of Cell Science.

[6]  Panagiotis K. Papasaikas,et al.  Genome-wide identification of Fas/CD95 alternative splicing regulators reveals links with iron homeostasis. , 2015, Molecular cell.

[7]  Chris Sander,et al.  Emerging landscape of oncogenic signatures across human cancers , 2013, Nature Genetics.

[8]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[9]  B. Frey,et al.  Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. , 2004, Molecular cell.

[10]  Hiroshi Kimura,et al.  Manipulation of Alternative Splicing by a Newly Developed Inhibitor of Clks* , 2004, Journal of Biological Chemistry.

[11]  Xiang-Dong Fu,et al.  Regulation of splicing by SR proteins and SR protein-specific kinases , 2013, Chromosoma.

[12]  Derek Y. Chiang,et al.  MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.

[13]  M. Hagiwara,et al.  Akt2 regulation of Cdc2-like kinases (Clk/Sty), serine/arginine-rich (SR) protein phosphorylation, and insulin-induced alternative splicing of PKCbetaII messenger ribonucleic acid. , 2009, Endocrinology.

[14]  Guey-Shin Wang,et al.  Splicing in disease: disruption of the splicing code and the decoding machinery , 2007, Nature Reviews Genetics.

[15]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[16]  Shawn M. Gomez,et al.  Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors , 2015, Oncotarget.

[17]  O. Elroy-Stein,et al.  Uncovering Hidden Layers of Cell Cycle Regulation through Integrative Multi-omic Analysis , 2015, PLoS genetics.

[18]  N. Sciaky,et al.  Symplekin Specifies Mitotic Fidelity by Supporting Microtubule Dynamics , 2010, Molecular and Cellular Biology.

[19]  B. Mack,et al.  EpCAM regulates cell cycle progression via control of cyclin D1 expression , 2013, Oncogene.

[20]  G. Biamonti,et al.  Phosphorylation of SRSF1 is modulated by replicational stress , 2011, Nucleic acids research.

[21]  G. Ghourab.  Oncogenes in cancer. , 1992, Advances in clinical chemistry.

[22]  Pamela A. Silver,et al.  An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis , 2010, Cell.

[23]  T. Pawson,et al.  The Protein Kinase Clk/Sty Directly Modulates SR Protein Activity: Both Hyper- and Hypophosphorylation Inhibit Splicing , 1999, Molecular and Cellular Biology.

[24]  D. M. Glover,et al.  Genome-wide survey of protein kinases required for cell cycle progression , 2004, Nature.

[25]  A. Gregory Matera,et al.  A day in the life of the spliceosome , 2014, Nature Reviews Molecular Cell Biology.

[26]  Michael J. Emanuele,et al.  A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells , 2014, eLife.

[27]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[28]  A. Schnittger,et al.  Cell cycle control across the eukaryotic kingdom. , 2013, Trends in cell biology.

[29]  A. Krainer,et al.  The gene encoding the splicing factor SF2/ASF is a proto-oncogene , 2007, Nature Structural &Molecular Biology.

[30]  Yumi Kim,et al.  CENP-E combines a slow, processive motor and a flexible coiled coil to produce an essential motile kinetochore tether , 2008, The Journal of cell biology.

[31]  J. Manley,et al.  Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. , 2010, Genes & development.

[32]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of clear cell renal cell carcinoma , 2013, Nature.

[33]  S. Geisler,et al.  Alternative splicing and mutation status of CHEK2 in stage III breast cancer , 2004, Oncogene.

[34]  R. Medema,et al.  Shared and separate functions of polo-like kinases and aurora kinases in cancer , 2010, Nature Reviews Cancer.

[35]  Michael R. Green,et al.  Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. , 2004, Molecular cell.

[36]  Damian Szklarczyk,et al.  Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing , 2011, Chemistry & biology.

[37]  E. Eyras,et al.  The translational landscape of the splicing factor SRSF1 and its role in mitosis , 2014, eLife.

[38]  A. Desai,et al.  Unstable microtubule capture at kinetochores depleted of the centromere‐associated protein CENP‐F , 2005, The EMBO journal.

[39]  E. Brambilla,et al.  Acetylation and phosphorylation of SRSF2 control cell fate decision in response to cisplatin , 2011, The EMBO journal.

[40]  C. Shin,et al.  The SR Protein SRp38 Represses Splicing in M Phase Cells , 2002, Cell.

[41]  D. Bates,et al.  Hallmarks of alternative splicing in cancer , 2014, Oncogene.

[42]  J. Skotheim,et al.  Control of cell cycle transcription during G1 and S phases , 2013, Nature Reviews Molecular Cell Biology.

[43]  W. Earnshaw,et al.  The chromosomal passenger complex (CPC): from easy rider to the godfather of mitosis , 2012, Nature Reviews Molecular Cell Biology.

[44]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[45]  I. Simon,et al.  Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells , 2008, Proceedings of the National Academy of Sciences.

[46]  J. Bell,et al.  In vivo regulation of alternative pre-mRNA splicing by the Clk1 protein kinase , 1997, Molecular and cellular biology.

[47]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[48]  J. Cáceres,et al.  The SR protein family of splicing factors: master regulators of gene expression. , 2009, The Biochemical journal.

[49]  Dan Chen,et al.  The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. , 2014, Cancer cell.

[50]  Robert J. Weatheritt,et al.  A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains , 2014, Cell.

[51]  William Arbuthnot Sir Lane,et al.  A serine kinase regulates intracellular localization of splicing factors in the cell cycle , 1994, Nature.

[52]  C. Burge,et al.  Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. , 2008, RNA.

[53]  C. Ball,et al.  Identification of genes periodically expressed in the human cell cycle and their expression in tumors. , 2002, Molecular biology of the cell.

[54]  P. Sharp,et al.  Detained introns are a novel, widespread class of post-transcriptionally spliced introns , 2015, Genes & development.

[55]  Jussi Taipale,et al.  Identification of pathways regulating cell size and cell-cycle progression by RNAi , 2006, Nature.

[56]  Sol Katzman,et al.  Frac-seq reveals isoform-specific recruitment to polyribosomes , 2013, Genome research.

[57]  J D Beggs,et al.  Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. , 2000, Genetics.

[58]  The Cancer Genome Atlas Research Network.  COMPREHENSIVE MOLECULAR CHARACTERIZATION OF CLEAR CELL RENAL CELL CARCINOMA , 2013, Nature.

[59]  Xiang-Dong Fu,et al.  SON controls cell-cycle progression by coordinated regulation of RNA splicing. , 2011, Molecular cell.

[60]  J. Valcárcel,et al.  The Ewing sarcoma protein regulates DNA damage-induced alternative splicing. , 2011, Molecular cell.

[61]  Katharine R. Grabek,et al.  Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator , 2015, eLife.

[62]  M. Hagiwara,et al.  Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor , 2011, The Journal of cell biology.

[63]  M. Lai,et al.  Differential effects of hyperphosphorylation on splicing factor SRp55. , 2003, The Biochemical journal.

[64]  Adam B. Olshen,et al.  The translational landscape of the mammalian cell cycle. , 2013, Molecular cell.