Pre-mRNA splicing and polyadenylation are critical steps in the maturation of eukaryotic mRNA. U1 snRNP is an essential component of the splicing machinery and participates in splice-site selection and spliceosome assembly by base-pairing to the 5′ splice site. U1 snRNP also plays an additional, nonsplicing global function in 3′ end mRNA processing; it actively suppresses the polyadenylation machinery from using early, mostly intronic polyadenylation signals which would lead to aberrant, truncated mRNAs. Thus, U1 snRNP safeguards pre-mRNA transcripts against premature polyadenylation and contributes to the regulation of alternative polyadenylation. Here, we review the role of U1 snRNP in 3′ end mRNA processing, outline the evidence that led to the recognition of its physiological, general role in inhibiting polyadenylation, and finally highlight the possibility of manipulating this U1 snRNP function for therapeutic purposes in cancer. 1. Introduction The generation of translationally competent messenger RNAs (mRNAs) is a complex molecular process that involves distinctive enzymatic reactions and dedicated cellular machineries that result in the splicing, capping, editing, and polyadenylation of a pre-mRNA transcript. During this process, the choice and usage of splice sites (alternative splicing, AS) and of polyadenylation signals (alternative polyadenylation, APA) within a common pre-mRNA can be differentially regulated depending on the developmental state, tissue, and cell type or in response to a variety of physiological stimuli or pathological conditions [1, 2]. Collectively, alternative splicing and polyadenylation are key molecular mechanisms for increasing the functional diversity of the human proteome, allowing the relatively small human genome (<25,000 genes) to generate an excess of 100,000 different protein isoforms [3]. However, because of the pervasiveness and essential role of AS in all physiological processes, aberrant RNA processing is also frequently associated with many diseases [4], and both AS and APA are deregulated and exploited by cancer cells to promote their growth and survival [5–7]. This review will focus on the recently described splicing-independent functions of U1 small ribonucleoprotein particle (snRNP) in pre-mRNA processing, with emphasis on its role in the regulation of APA site selection and in the suppression of intronic polyadenylation (IPA). Furthermore, we will address innovative approaches to leverage U1 snRNP functions as therapeutic avenues in cancer treatment. 2. U1 snRNP Canonical Role in Splicing: A Harbinger
References
[1]
A. Kalsotra and T. A. Cooper, “Functional consequences of developmentally regulated alternative splicing,” Nature Reviews Genetics, vol. 12, no. 10, pp. 715–729, 2011.
[2]
A. R. Kornblihtt, I. E. Schor, M. Allo, G. Dujardin, E. Petrillo, et al., “Alternative splicing: a pivotal step between eukaryotic transcription and translation,” Nature Reviews Molecular Cell Biology, vol. 14, pp. 153–165, 2013.
[3]
T. W. Nilsen and B. R. Graveley, “Expansion of the eukaryotic proteome by alternative splicing,” Nature, vol. 463, no. 7280, pp. 457–463, 2010.
[4]
L. Cartegni, S. L. Chew, and A. R. Krainer, “Listening to silence and understanding nonsense: exonic mutations that affect splicing,” Nature Reviews Genetics, vol. 3, no. 4, pp. 285–298, 2002.
[5]
R. K. Singh and T. A. Cooper, “Pre-mRNA splicing in disease and therapeutics,” Trends in Molecular Medicine, vol. 18, no. 8, pp. 472–482, 2012.
[6]
C. Ghigna, C. Valacca, and G. Biamonti, “Alternative splicing and tumor progression,” Current Genomics, vol. 9, no. 8, pp. 556–570, 2008.
[7]
R. Elkon, A. P. Ugalde, and R. Agami, “Alternative cleavage and polyadenylation: extent, regulation and function,” Nature Reviews Genetics, vol. 14, pp. 496–506, 2013.
[8]
M. C. Wahl, C. L. Will, and R. Lührmann, “The spliceosome: design principles of a dynamic RNP machine,” Cell, vol. 136, no. 4, pp. 701–718, 2009.
[9]
X. Roca, A. R. Krainer, and I. C. Eperon, “Pick one, but be quick: 5' splice sites and the problems of too many choices,” Genes & Development, vol. 27, pp. 129–144, 2013.
[10]
S. J. Beserga and J. A. Steitz, “The diverse world of small ribonucleoproteins,” in The RNA World. Cold Spring Harbor, R. F. Gesteland and J. F. Atkins, Eds., pp. 359–381, CSHL Press, 1993.
[11]
R. Reddy and H. Busch, “RNA sequences, structure, and modifications,” in Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles, M. Birnstiel, Ed., pp. 1–37, Springer, New York, NY, USA, 1988.
[12]
K. M. Wassarman and J. A. Steitz, “Association with terminal exons in pre-mRNAs: a new role for the U1 snRNP?” Genes and Development, vol. 7, no. 4, pp. 647–659, 1993.
[13]
W. C. Boelens, E. J. R. Jansen, W. J. Van Venrooij, R. Stripecke, I. W. Mattal, and S. I. Gunderson, “The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA,” Cell, vol. 72, no. 6, pp. 881–892, 1993.
[14]
N. J. Proudfoot, “Ending the message: poly(A) signals then and now,” Genes and Development, vol. 25, no. 17, pp. 1770–1782, 2011.
[15]
B. Tian, J. Hu, H. Zhang, and C. S. Lutz, “A large-scale analysis of mRNA polyadenylation of human and mouse genes,” Nucleic Acids Research, vol. 33, no. 1, pp. 201–212, 2005.
[16]
F. Ozsolak, P. Kapranov, S. Foissac et al., “Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation,” Cell, vol. 143, no. 6, pp. 1018–1029, 2010.
[17]
B. Tian, Z. Pan, and Y. L. Ju, “Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing,” Genome Research, vol. 17, no. 2, pp. 156–165, 2007.
[18]
B. Tian and J. L. Manley, “Alternative cleavage and polyadenylation: the long and short of it,” Trends in Biochemical Sciences, vol. 38, no. 6, pp. 312–320, 2013.
[19]
S. Vorlová, G. Rocco, C. V. LeFave et al., “Induction of antagonistic soluble decoy receptor tyrosine kinases by intronic polya activation,” Molecular Cell, vol. 43, no. 6, pp. 927–939, 2011.
[20]
N. Spies, C. B. Nielsen, R. A. Padgett, and C. B. Burge, “Biased chromatin signatures around polyadenylation sites and exons,” Molecular Cell, vol. 36, no. 2, pp. 245–254, 2009.
[21]
A. R. Morris, A. Bos, B. Diosdado, K. Rooijers, R. Elkon, et al., “Alternative cleavage and polyadenylation during colorectal cancer development,” Clinical Cancer Research, vol. 18, pp. 5256–5266, 2012.
[22]
Y. Fu, Y. Sun, Y. Li et al., “Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing,” Genome Research, vol. 21, no. 5, pp. 741–747, 2011.
[23]
C. Mayr and D. P. Bartel, “Widespread shortening of 3' UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells,” Cell, vol. 138, no. 4, pp. 673–684, 2009.
[24]
R. Sandberg, J. R. Neilson, A. Sarma, P. A. Sharp, and C. B. Burge, “Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites,” Science, vol. 320, no. 5883, pp. 1643–1647, 2008.
[25]
K. E. Knudsen, “The cyclin D1b splice variant: an old oncogene learns new tricks,” Cell Division, vol. 1, article 15, 2006.
[26]
R. J. C. Albuquerque, T. Hayashi, W. G. Cho et al., “Alternatively spliced vascular endothelial growth factor receptor-2 is an essential endogenous inhibitor of lymphatic vessel growth,” Nature Medicine, vol. 15, no. 9, pp. 1023–1030, 2009.
[27]
J. Becker, H. Pavlakovic, F. Ludewig et al., “Neuroblastoma progression correlates with downregulation of the lymphangiogenesis inhibitor sVEGFR-2,” Clinical Cancer Research, vol. 16, no. 5, pp. 1431–1441, 2010.
[28]
F. A. Bava, C. Eliscovich, P. G. Ferreira, B. Minana, C. Ben-Dov, et al., “CPEB1 coordinates alternative 3'-UTR formation with translational regulation,” Nature, vol. 495, no. 7439, pp. 121–125, 2013.
[29]
S. Danckwardt, I. Kaufmann, M. Gentzel et al., “Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals,” EMBO Journal, vol. 26, no. 11, pp. 2658–2669, 2007.
[30]
A. Moreira, Y. Takagaki, S. Brackenridge, M. Wollerton, J. L. Manley, and N. J. Proudfoot, “The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3' end formation by two distinct mechanisms,” Genes and Development, vol. 12, no. 16, pp. 2522–2534, 1998.
[31]
P. Castelo-Branco, A. Furger, M. Wollerton, C. Smith, A. Moreira, and N. Proudfoot, “Erratum: polypyrimidine tract binding protein modulates efficiency of polyadenylation,” Molecular and Cellular Biology, vol. 24, no. 15, pp. 4174–4183, 2004.
[32]
C. L. Moore and P. A. Sharp, “Site-specific polyadenylation in a cell-free reaction,” Cell, vol. 36, no. 3, pp. 581–591, 1984.
[33]
C. L. Moore and P. A. Sharp, “Accurate cleavage and polyadenylation of exogenous RNA substrate,” Cell, vol. 41, no. 3, pp. 845–855, 1985.
[34]
C. Hashimoto and J. A. Steitz, “A small nuclear ribonucleoprotein associates with the AAUAAA polyadenylation signal in vitro,” Cell, vol. 45, no. 4, pp. 581–591, 1986.
[35]
C. W. G. Van Gelder, S. I. Gunderson, E. J. R. Jansen et al., “A complex secondary structure in U1A pre-mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation,” EMBO Journal, vol. 12, no. 13, pp. 5191–5200, 1993.
[36]
S. I. Gunderson, K. Beyer, G. Martin, W. Keller, W. C. Boelens, and I. W. Mattaj, “The human U1A snRNP protein regulates polyadenylation via a direct interaction with poly(A) polymerase,” Cell, vol. 76, no. 3, pp. 531–541, 1994.
[37]
C. Phillips, S. Jung, and S. I. Gunderson, “Regulation of nuclear poly(A) addition controls the expression of immunoglobulin M secretory mRNA,” EMBO Journal, vol. 20, no. 22, pp. 6443–6452, 2001.
[38]
C. Phillips, N. Pachikara, and S. I. Gunderson, “U1A inhibits cleavage at the immunoglobulin M heavy-chain secretory poly(A) site by binding between the two downstream GU-rich regions,” Molecular and Cellular Biology, vol. 24, no. 14, pp. 6162–6171, 2004.
[39]
J. Ma, S. I. Gunderson, and C. Phillips, “Non-snRNP U1A levels decrease during mammalian B-cell differentiation and release the IgM secretory poly(A) site from repression,” RNA, vol. 12, no. 1, pp. 122–132, 2006.
[40]
P. A. Furth, W.-T. Choe, J. H. Rex, J. C. Byrne, and C. C. Baker, “Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions,” Molecular and Cellular Biology, vol. 14, no. 8, pp. 5278–5289, 1994.
[41]
S. I. Gunderson, M. Polycarpou-Schwarz, and I. W. Mattaj, “U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase,” Molecular Cell, vol. 1, no. 2, pp. 255–264, 1998.
[42]
M. P. Ashe, A. Furger, and N. J. Proudfoot, “Stem-loop 1 of the U1 snRNP plays a critical role in the suppression of HIV-1 polyadenylation,” RNA, vol. 6, no. 2, pp. 170–177, 2000.
[43]
M. P. Ashe, L. H. Pearson, and N. J. Proudfoot, “The HIV-1 5' LTR poly (A) site is inactivated by U1 snRNP interaction with the downstream major splice donor site,” EMBO Journal, vol. 16, no. 18, pp. 5752–5763, 1997.
[44]
S. A. Beckley, P. Liu, M. L. Stover, S. I. Gunderson, A. C. Lichtler, and D. W. Rowe, “Reduction of target gene expression by a modified U1 snRNA,” Molecular and Cellular Biology, vol. 21, no. 8, pp. 2815–2825, 2001.
[45]
P. Fortes, Y. Cuevas, F. Guan et al., “Inhibiting expression of specific genes in mammalian cells with 5′ end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-MRNA,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 14, pp. 8264–8269, 2003.
[46]
X. Abad, M. Vera, S. P. Jung et al., “Requirements for gene silencing mediated by U1 snRNA binding to a target sequence,” Nucleic Acids Research, vol. 36, no. 7, pp. 2338–2352, 2008.
[47]
R. Goraczniak, M. A. Behlke, and S. I. Gunderson, “Gene silencing by synthetic U1 Adaptors,” Nature Biotechnology, vol. 27, no. 3, pp. 257–263, 2009.
[48]
D. Kaida, M. G. Berg, I. Younis et al., “U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation,” Nature, vol. 468, no. 7324, pp. 664–668, 2010.
[49]
A. E. Almada, X. Wu, A. J. Kriz, C. B. Burge, and P. A. Sharp, “Promoter directionality is controlled by U1 snRNP and polyadenylation signals,” Nature, vol. 2013, 2013.
[50]
M. G. Berg, L. N. Singh, I. Younis, Q. Liu, A. M. Pinto, et al., “U1 snRNP determines mRNA length and regulates isoform expression,” Cell, vol. 150, pp. 53–64, 2012.
[51]
X. Roca and A. R. Krainer, “Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA,” Nature Structural and Molecular Biology, vol. 16, no. 2, pp. 176–182, 2009.
[52]
X. H.-F. Zhang, K. A. Heller, I. Hefter, C. S. Leslie, and L. A. Chasin, “Sequence information for the splicing of human pre-mRNA identified by support vector machine classification,” Genome Research, vol. 13, no. 12, pp. 2637–2650, 2003.
[53]
F. Lejeune and L. E. Maquat, “Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells,” Current Opinion in Cell Biology, vol. 17, no. 3, pp. 309–315, 2005.
[54]
M. Graille and B. Seraphin, “Surveillance pathways rescuing eukaryotic ribosomes lost in translation,” Nature Reviews Molecular Cell Biology, vol. 13, pp. 727–735, 2012.
[55]
L. Spraggon and L. Cartegni, “Antisense modulation of RNA processing as a therapeutic approach in cancer therapy,” Drug Discovery Today, 2013.
[56]
R. Goraczniak, B. A. Wall, M. A. Behlke, K. A. Lennox, E. S. Ho, et al., “U1 adaptor oligonucleotides targeting BCL2 and GRM1 suppress growth of human melanoma xenografts in vivo,” Molecular Therapy, vol. 2, p. e92, 2013.
[57]
J. L. F. Teh and S. Chen, “Glutamatergic signaling in cellular transformation,” Pigment Cell and Melanoma Research, vol. 25, pp. 331–342, 2012.
[58]
T. D. Prickett and Y. Samuels, “Molecular pathways: dysregulated glutamatergic signaling pathways in cancer,” Clinical Cancer Research, vol. 18, pp. 4240–4246, 2012.
[59]
R. J. Youle and A. Strasser, “The BCL-2 protein family: opposing activities that mediate cell death,” Nature Reviews Molecular Cell Biology, vol. 9, no. 1, pp. 47–59, 2008.
[60]
E. Ruoslahti, “RGD and other recognition sequences for integrins,” Annual Review of Cell and Developmental Biology, vol. 12, pp. 697–715, 1996.
[61]
U. Weirauch, A. Grünweller, L. Cuellar, R. K. Hartmann, and A. Aigner, “U1 adaptors for the therapeutic knockdown of the oncogene pim-1 kinase in glioblastoma,” Nucleic Acid Therapeutics, vol. 23, no. 4, pp. 264–272, 2013.
[62]
T. Zhang, X. Zhang, K. Ding, K. Yang, Z. Zhang, and Y. Xu, “PIM-1 gene RNA interference induces growth inhibition and apoptosis of prostate cancer cells and suppresses tumor progression in vivo,” Journal of Surgical Oncology, vol. 101, no. 6, pp. 513–519, 2010.
[63]
T. A. Vickers, M. Sabripour, and S. T. Crooke, “U1 adaptors result in reduction of multiple pre-mRNA species principally by sequestering U1snRNP,” Nucleic Acids Research, vol. 39, no. 10, p. e71, 2011.
[64]
M. A. Havens, D. M. Duelli, and M. L. Hastings, “Targeting RNA splicing for disease therapy,” RNA, vol. 4, no. 3, pp. 247–266, 2013.
[65]
F. Zammarchi, E. De Stanchina, E. Bournazou et al., “Antitumorigenic potential of STAT3 alternative splicing modulation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 43, pp. 17779–17784, 2011.
[66]
A. Gschwind, O. M. Fischer, and A. Ullrich, “The discovery of receptor tyrosine kinases: targets for cancer therapy,” Nature Reviews Cancer, vol. 4, no. 5, pp. 361–370, 2004.
[67]
M. A. Lemmon and J. Schlessinger, “Cell signaling by receptor tyrosine kinases,” Cell, vol. 141, no. 7, pp. 1117–1134, 2010.
[68]
Y. Yarden and G. Pines, “The ERBB network: at last, cancer therapy meets systems biology,” Nature Reviews Cancer, vol. 12, pp. 553–563, 2012.
[69]
Z. Tiran, A. Oren, C. Hermesh et al., “A novel recombinant soluble splice variant of met is a potent antagonist of the hepatocyte growth factor/scatter factor-met pathway,” Clinical Cancer Research, vol. 14, no. 14, pp. 4612–4621, 2008.
[70]
K. K. Ciombor, J. Berlin, and E. Chan, “Aflibercept,” Clinical Cancer Research, vol. 19, pp. 1920–1925, 2013.
[71]
L. Claesson-Welsh and M. Welsh, “VEGFA and tumour angiogenesis,” Journal of Internal Medicine, vol. 273, no. 2, pp. 114–127, 2013.
[72]
L. A. Owen, H. Uehara, J. Cahoon, W. Huang, J. Simonis, and B. K. Ambati, “Morpholino-mediated increase in soluble flt-1 expression results in decreased ocular and tumor neovascularization,” PLoS ONE, vol. 7, no. 3, Article ID e33576, 2012.