The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation
详细信息    查看全文
  • 作者:Ryan Davis (1)
    Yongsheng Shi (1)
  • 关键词:mRNA ; Alternative polyadenylation (APA) ; Polyadenylation site (PAS) ; Q344+.14 ; ; /li> ; mRNA
  • 刊名:Journal of Zhejiang University SCIENCE B
  • 出版年:2014
  • 出版时间:May 2014
  • 年:2014
  • 卷:15
  • 期:5
  • 页码:429-437
  • 全文大小:
  • 参考文献:1. Alkan, S.A., Martincic, K., Milcarek, C., 2006. The hnRNPs F and H2 bind to similar sequences to influence gene expression. / Biochem. J., 393(1):361-71. [doi:10.1042/BJ20050538] CrossRef
    2. An, J.J., Gharami, K., Liao, G.Y., / et al., 2008. Distinct role of long 3-UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. / Cell, 134(1): 175-87. [doi:10.1016/j.cell.2008.05.045] CrossRef
    3. Arhin, G.K., Boots, M., Bagga, P.S., / et al., 2002. Downstream sequence elements with different affinities for the hnRNP H/H-protein influence the processing efficiency of mammalian polyadenylation signals. / Nucl. Acids Res., 30(8):1842-850. [doi:10.1093/nar/30.8.1842] CrossRef
    4. Bava, F.A., Eliscovich, C., Ferreira, P.G., / et al., 2013. CPEB1 coordinates alternative 3-UTR formation with translational regulation. / Nature, 495(7439):121-25. [doi:10.1038/nature11901] CrossRef
    5. Bentley, D.L., 2005. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. / Curr. Opin. Cell Biol., 17(3):251-56. [doi:10.1016/j.ceb.2005.04.006] CrossRef
    6. Boelens, W.C., Jansen, E.J., van Venrooij, W.J., / et al., 1993. The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA. / Cell, 72(6): 881-92. [doi:10.1016/0092-8674(93)90577-D] CrossRef
    7. Boutet, S.C., Cheung, T.H., Quach, N.L., / et al., 2012. Alternative polyadenylation mediates microRNA regulation of muscle stem cell function. / Cell Stem Cell, 10(3):327-36. [doi:10.1016/j.stem.2012.01.017] CrossRef
    8. Brais, B., 2009. Oculopharyngeal muscular dystrophy: a polyalanine myopathy. / Curr. Neurol. Neurosci. Rep., 9(1): 76-2. [doi:10.1007/s11910-009-0012-y] CrossRef
    9. Brown, S.J., Stoilov, P., Xing, Y., 2012. Chromatin and epigenetic regulation of pre-mRNA processing. / Hum. Mol. Genet., 21(R1):R90. [doi:10.1093/hmg/dds353] CrossRef
    10. Castelo-Branco, P., Furger, A., Wollerton, M., / et al., 2004. Polypyrimidine tract binding protein modulates efficiency of polyadenylation. / Mol. Cell. Biol., 24(10):4174-183. [doi:10.1128/MCB.24.10.4174-4183.2004] CrossRef
    11. Chan, S., Choi, E.A., Shi, Y., 2011. Pre-mRNA 3-end processing complex assembly and function. / Wiley Interdiscip. Rev. RNA, 2(3):321-35. [doi:10.1002/wrna.54] CrossRef
    12. Chuvpilo, S., Zimmer, M., Kerstan, A., / et al., 1999. Alternative polyadenylation events contribute to the induction of NF-ATc in effector T cells. / Immunity, 10(2):261-69. [doi:10.1016/S1074-7613(00)80026-6] CrossRef
    13. Colgan, D.F., Manley, J.L., 1997. Mechanism and regulation of mRNA polyadenylation. / Genes Dev., 11(21):2755-766. [doi:10.1101/gad.11.21.2755] CrossRef
    14. Cowley, M., Wood, A.J., Bohm, S., / et al., 2012. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. / Nucl. Acids Res., 40(18):8917-926. [doi:10.1093/nar/gks654] CrossRef
    15. Danckwardt, S., Hentze, M.W., Kulozik, A.E., 2008. 3-end mRNA processing: molecular mechanisms and implications for health and disease. / EMBO J., 27(3):482-98. [doi:10.1038/sj.emboj.7601932] CrossRef
    16. Danckwardt, S., Gantzert, A.S., Macher-Goeppinger, S., / et al., 2011. p38 MAPK controls prothrombin expression by regulated RNA 3-end processing. / Mol. Cell, 41(3): 298-10. [doi:10.1016/j.molcel.2010.12.032] CrossRef
    17. de Klerk, E., Venema, A., Anvar, S.Y., / et al., 2012. Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation. / Nucl. Acids Res., 40(18):9089. [doi:10.1093/nar/gks655] CrossRef
    18. Denome, R.M., Cole, C.N., 1988. Patterns of polyadenylation site selection in gene constructs containing multiple polyadenylation signals. / Mol. Cell Biol., 8:4829-839.
    19. Derti, A., Garrett-Engele, P., Macisaac, K.D., / et al., 2012. A quantitative atlas of polyadenylation in five mammals. / Genome Res., 22(6):1173-183. [doi:10.1101/gr.132563.111] CrossRef
    20. Dittmar, K.A., Jiang, P., Park, J.W., / et al., 2012. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. / Mol. Cell. Biol., 32(8):1468-482. [doi:10.1128/MCB.06536-11] CrossRef
    21. Elkon, R., Drost, J., van Haaften, G., / et al., 2012. E2F mediates enhanced alternative polyadenylation in proliferation. / Genome Biol., 13(7):R59. [doi:10.1186/gb-2012-13-7-r59] CrossRef
    22. Elkon, R., Ugalde, A.P., Agami, R., 2013. Alternative cleavage and polyadenylation: extent, regulation and function. / Nat. Rev. Genet., 14(7):496-06. [doi:10.1038/nrg3482] CrossRef
    23. Flavell, S.W., Kim, T.K., Gray, J.M., / et al., 2008. Genomewide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. / Neuron, 60(6):1022-038. [doi:10.1016/j.neuron.2008.11.029] CrossRef
    24. Fu, Y., Sun, Y., Li, Y., / et al., 2011. Differential genome-wide profiling of tandem 3-UTRs among human breast cancer and normal cells by high-throughput sequencing. / Genome Res., 21(5):741-47. [doi:10.1101/gr.115295.110] CrossRef
    25. Gawande, B., Robida, M.D., Rahn, A., / et al., 2006. / Drosophila Sex-lethal protein mediates polyadenylation switching in the female germline. / EMBO J., 25(6):1263-272. [doi:10.1038/sj.emboj.7601022] CrossRef
    26. Hirose, Y., Manley, J.L., 2000. RNA polymerase II and the integration of nuclear events. / Genes Dev., 14:1415-429.
    27. Jan, C.H., Friedman, R.C., Ruby, J.G., / et al., 2010. Formation, regulation and evolution of / Caenorhabditis elegans 3′UTRs. / Nature, 469(7328):97-01. [doi:10.1038/nature09616] CrossRef
    28. Jenal, M., Elkon, R., Loayza-Puch, F., / et al., 2012. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. / Cell, 149(3):538-53. [doi:10.1016/j.cell.2012.03.022] CrossRef
    29. Ji, X., Wan, J., Vishnu, M., / et al., 2013. αCP poly(C) binding proteins act as global regulators of alternative polyadenylation. / Mol. Cell. Biol., 33(13):2560-573. [doi:10.1128/MCB.01380-12] CrossRef
    30. Ji, Z., Tian, B., 2009. Reprogramming of 3-untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. / PLoS ONE, 4(12):e8419. [doi:10.1371/journal.pone.0008419] CrossRef
    31. Ji, Z., Lee, J.Y., Pan, Z., / et al., 2009. Progressive lengthening of 3-untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. / PNAS, 106(17):7028-033. [doi:10.1073/pnas.0900028106] CrossRef
    32. Juge, F., Audibert, A., Benoit, B., / et al., 2000. Tissue-specific autoregulation of / Drosophila suppressor of forked by alternative poly(A) site utilization leads to accumulation of the suppressor of forked protein in mitotically active cells. / RNA, 6(11):1529-538. [doi:10.1017/S1355838200001266] CrossRef
    33. Kleiman, F.E., Manley, J.L., 2001. The BARD1-CstF-50 interaction links mRNA 3-end formation to DNA damage and tumor suppression. / Cell, 104(5):743-53. [doi:10.1016/S0092-8674(01)00270-7] CrossRef
    34. Lackford, B., Yao, C., Charles, G.M., / et al., 2014. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. / EMBO J., 33(8):878-89. [doi:10.1002/embj.201386537] CrossRef
    35. Lianoglou, S., Garg, V., Yang, J.L., / et al., 2013. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. / Genes Dev., 27(21): 2380-396. [doi:10.1101/gad.229328.113] CrossRef
    36. Liao, G.Y., An, J.J., Gharami, K., / et al., 2012. Dendritically targeted / Bdnf mRNA is essential for energy balance and response to leptin. / Nat. Med., 18(4):564-71. [doi:10.1038/nm.2687] CrossRef
    37. Luo, W., Ji, Z., Pan, Z., / et al., 2013. The conserved intronic cleavage and polyadenylation site of / CstF-77 gene imparts control of 3-end processing activity through feedback autoregulation and by U1 snRNP. / PLoS Genet., 9(7): e1003613. [doi:10.1371/journal.pgen.1003613] CrossRef
    38. Martin, G., Gruber, A.R., Keller, W., / et al., 2012. Genomewide analysis of pre-mrna 3-end processing reveals a decisive role of human cleavage factor I in the regulation of 3-UTR length. / Cell Rep., 1(6):753-63. [doi:10.1016/j.celrep.2012.05.003] CrossRef
    39. Martincic, K., Campbell, R., Edwalds-Gilbert, G., / et al., 1998. Increase in the 64-kDa subunit of the polyadenylation/cleavage stimulatory factor during the G0 to S phase transition. / PNAS, 95(19):11095-1100. [doi:10.1073/pnas.95.19.11095] CrossRef
    40. Mayr, C., Bartel, D.P., 2009. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. / Cell, 138(4):673-84. [doi:10.1016/j.cell.2009.06.016] CrossRef
    41. Mueller, A.A., Cheung, T.H., Rando, T.A., 2013. All’s well that ends well: alternative polyadenylation and its implications for stem cell biology. / Curr. Opin. Cell Biol., 25(2): 222-32. [doi:10.1016/j.ceb.2012.12.008] CrossRef
    42. Muoz, M.J., Pérez Santangelo, M.S., Paronetto, M.P., / et al., 2009. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. / Cell, 137(4): 708-20. [doi:10.1016/j.cell.2009.03.010] CrossRef
    43. Ozsolak, F., Kapranov, P., Foissac, S., / et al., 2010. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. / Cell, 143(6): 1018-029. [doi:10.1016/j.cell.2010.11.020] CrossRef
    44. Pan, Z., Zhang, H., Hague, L.K., / et al., 2006. An intronic polyadenylation site in human and mouse / CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. / Gene, 366(2):325-34. [doi:10.1016/j.gene.2005.09.024] CrossRef
    45. Park, J.Y., Li, W., Zheng, D., / et al., 2011. Comparative analysis of mRNA isoform expression in cardiac hypertrophy and development reveals multiple post-transcriptional regulatory modules. / PLoS ONE, 6(7):e22391. [doi:10.1371/journal.pone.0022391] CrossRef
    46. Pinto, P.A., Henriques, T., Freitas, M.O., / et al., 2011. RNA polymerase II kinetics in / polo polyadenylation signal selection. / EMBO J., 30(12):2431-444. [doi:10.1038/emboj.2011.156] CrossRef
    47. Proudfoot, N.J., Furger, A., Dye, M.J., 2002. Integrating mRNA processing with transcription. / Cell, 108(4):501-12. [doi:10.1016/S0092-8674(02)00617-7] CrossRef
    48. Sandberg, R., Neilson, J.R., Sarma, A., / et al., 2008. Proliferating cells express mRNAs with shortened 3-untranslated regions and fewer microRNA target sites. / Science, 320(5883):1643-647. [doi:10.1126/science.1155390] CrossRef
    49. Shepard, P.J., Choi, E.A., Lu, J., / et al., 2011. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. / RNA, 17(4):761-72. [doi:10.1261/rna.2581711] CrossRef
    50. Shi, Y., 2012. Alternative polyadenylation: new insights from global analyses. / RNA, 18(12):2105-117. [doi:10.1261/rna.035899.112] CrossRef
    51. Shi, Y., Di Giammartino, D.C., Taylor, D., / et al., 2009. Molecular architecture of the human pre-mRNA 3-processing complex. / Mol. Cell, 33(3):365-76. [doi:10.1016/j.molcel.2008.12.028] CrossRef
    52. Smibert, P., Miura, P., Westholm, J.O., / et al., 2012. Global patterns of tissue-specific alternative polyadenylation in / Drosophila. / Cell Rep., 1(3):277-89. [doi:10.1016/j.celrep.2012.01.001] CrossRef
    53. Spies, N., Burge, C.B., Bartel, D.P., 2013. 3-UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. / Genome Res., 23(12):2078-090. [doi:10.1101/gr.156919. 113] CrossRef
    54. Takagaki, Y., Manley, J.L., 1998. Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation. / Mol. Cell, 2(6):761-71. [doi:10.1016/S1097-2765(00)80291-9] CrossRef
    55. Takagaki, Y., Seipelt, R.L., Peterson, M.L., / et al., 1996. The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. / Cell, 87(5):941-52. [doi:10.1016/S0092-8674(00)82000-0] CrossRef
    56. Tian, B., Graber, J.H., 2012. Signals for pre-mRNA cleavage and polyadenylation. / Wiley Interdiscip. Rev. RNA, 3(3): 385-96. [doi:10.1002/wrna.116] CrossRef
    57. Tian, B., Manley, J.L., 2013. Alternative cleavage and polyadenylation: the long and short of it. / Trends Biochem. Sci., 38(6):312. [doi:10.1016/j.tibs.2013.03.005] CrossRef
    58. Ulitsky, I., Shkumatava, A., Jan, C.H., / et al., 2012. Extensive alternative polyadenylation during zebrafish development. / Genome Res., 22(10):2054-066. [doi:10.1101/gr.139733.112] CrossRef
    59. Vagner, S., Ruegsegger, U., Gunderson, S.I., / et al., 2000. Position-dependent inhibition of the cleavage step of pre-mRNA 3-end processing by U1 snRNP. / RNA, 6(2): 178-88. CrossRef
    60. Wood, A.J., Schulz, R., Woodfine, K., / et al., 2008. Regulation of alternative polyadenylation by genomic imprinting. / Genes Dev., 22(9):1141-146. [doi:10.1101/gad.473408] CrossRef
    61. Yao, C., Biesinger, J., Wan, J., / et al., 2012. Transcriptomewide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. / PNAS, 109(46):18773-8778. [doi:10.1073/pnas.1211101109] CrossRef
    62. Yao, C., Choi, E.A., Weng, L., / et al., 2013. Overlapping and distinct functions of CstF64 and CstF64tau in mammalian mRNA 3-processing. / RNA, 19(12):1781-790. [doi:10.1261/rna.042317.113] CrossRef
    63. Yu, L., Volkert, M.R., 2013. UV damage regulates alternative polyadenylation of the / RPB2 gene in yeast. / Nucl. Acids Res., 41(5):3104-114. [doi:10.1093/nar/gkt020] CrossRef
    64. Zhao, J., Hyman, L., Moore, C., 1999. Formation of mRNA 3-ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. / Microbiol. Mol. Biol. Rev., 63(2):405-45.
  • 作者单位:Ryan Davis (1)
    Yongsheng Shi (1)

    1. Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, 92697, USA
  • ISSN:1862-1783
文摘
The majority of eukaryotic genes produce multiple mRNA isoforms with distinct 3-ends through a process called mRNA alternative polyadenylation (APA). Recent studies have demonstrated that APA is dynamically regulated during development and in response to environmental stimuli. A number of mechanisms have been described for APA regulation. In this review, we attempt to integrate all the known mechanisms into a unified model. This model not only explains most of previous results, but also provides testable predictions that will improve our understanding of the mechanistic details of APA regulation. Finally, we briefly discuss the known and putative functions of APA regulation.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700