References
- Barabino, S.M.L., and Keller, W. (1999). Last but not least: fegulated Poly(A) tail formation. Cell 99, 9-11. https://doi.org/10.1016/S0092-8674(00)80057-4
- Bava, F., Eliscovich, C., Ferreira, P.G., Minana, B., Ben-Dov, C., Guigo, R., Valcarcel, J., and Mendez, R. (2013). CPEB1 coordinates alternative 3prime]-UTR formation with translational regulation. Nature 495, 121-125. https://doi.org/10.1038/nature11901
- Beaudoing, E., Freier, S., Wyatt, J.R., Claverie, J., and Gautheret, D. (2000). Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10, 1001-1010. https://doi.org/10.1101/gr.10.7.1001
- Beisang, D., Reilly, C., and Bohjanen, P.R. (2014). Alternative polyadenylation regulates CELF1/CUGBP1 target transcripts following T cell activation. Gene 550, 93-100. https://doi.org/10.1016/j.gene.2014.08.021
- Boutet, S., Cheung, T., Quach, N., Liu, L., Prescott, S.L., Edalati, A., Iori, K., and Rando, T. (2012). Alternative polyadenylation mediates microRNA regulation of muscle stem cell function. Cell Stem Cell 10, 327-336. https://doi.org/10.1016/j.stem.2012.01.017
- Chang, J., Zhang, W., Yeh, H., de Jong, E.P., Jun, S., Kim, K., Bae, S.S., Beckman, K., Hwang, T.H., Kim, K., et al. (2015). mRNA 3prime]-UTR shortening is a molecular signature of mTORC1 activation. Nat. Commun. 6, 7218.
- Chuvpilo, S., Zimmer, M., Kerstan, A., Glockner, J., Avots, A., Escher, C., Fischer, C., Inashkina, I., Jankevics, E., Berberich- Siebelt, F., et al. (1999). Alternative polyadenylation events contribute to the induction of NF-ATc in effector T cells. Immunity 10, 261-269. https://doi.org/10.1016/S1074-7613(00)80026-6
- Colgan, D.F., and Manley, J.L. (1997). Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11, 2755-2766. https://doi.org/10.1101/gad.11.21.2755
- Danckwardt, S., Hentze, M.W., and Kulozik, A.E. (2007a). 3ae end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J. 27, 482-498.
- Danckwardt, S., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A., Gehring, N.H., Neu‐Yilik, G., Bork, P., Keller, W., Wilm, M., et al. (2007b). Splicing factors stimulate polyadenylation via USEs at non‐canonical 3′ end formation signals. EMBO J. 26, 2658-2669. https://doi.org/10.1038/sj.emboj.7601699
- de Klerk, E., Venema, A., Anvar, S.Y., Goeman, J.J., Hu, O., Trollet, C., Dickson, G., den Dunnen, J.T., van der Maarel, S.M., Raz, V., et al. (2012). Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation. Nucleic Acids Res. 40, 9089-9101. https://doi.org/10.1093/nar/gks655
- Di Giammartino, D.C., Nishida, K., and Manley, J.L. (2011). Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866. https://doi.org/10.1016/j.molcel.2011.08.017
- Elkon, R., Drost, J., van Haaften, G., Jenal, M., Schrier, M., Oude Vrielink, J., and Agami, R. (2012). E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol. 13, R59. https://doi.org/10.1186/gb-2012-13-7-r59
- Elkon, R., Ugalde, A.P., and Agami, R. (2013). Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14, 496-506. https://doi.org/10.1038/nrg3482
- Fabian, M.R., Sonenberg, N., and Filipowicz, W. (2010). Regulation of mRNA Translation and Stability by microRNAs. Annu. Rev. Biochem. 79, 351-379. https://doi.org/10.1146/annurev-biochem-060308-103103
- Graber, J.H., Cantor, C.R., Mohr, S.C., and Smith, T.F. (1999). Genomic detection of new yeast pre-mRNA 3'-end-processing signals. Nucleic Acids Res. 27, 888-894. https://doi.org/10.1093/nar/27.3.888
- Han, T., Kato, M., Xie, S., Wu, L., Mirzaei, H., Pei, J., Chen, M., Xie, Y., Allen, J., Xiao, G., et al. (2012). Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell 149, 768-779. https://doi.org/10.1016/j.cell.2012.04.016
- Hoque, M., Ji, Z., Zheng, D., Luo, W., Li, W., You, B., Park, J.Y., Yehia, G., and Tian, B. (2013). Analysis of alternative cleavage and polyadenylation by 3prime] region extraction and deep sequencing. Nat. Meth. 10, 133-139. https://doi.org/10.1038/nchembio.1406
- Jenal, M., Elkon, R., Loayza-Puch, F., van Haaften, G., Kühn, U., Menzies, F., Vrielink, J.F., Bos, A., Drost, J., Rooijers, K., et al. (2012). The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 149, 538-553. https://doi.org/10.1016/j.cell.2012.03.022
- Ji, Z., and 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, e8419. https://doi.org/10.1371/journal.pone.0008419
- Ji, Z., Lee, J.Y., Pan, Z., Jiang, B., and Tian, B. (2009). Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl. Acad. Sci. 106, 7028-7033. https://doi.org/10.1073/pnas.0900028106
- Kuhn, U., Gundel, M., Knoth, A., Kerwitz, Y., Rüdel, S., and Wahle, E. (2009). Poly(A) tail length is controlled by the nuclear poly(A)- binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. J. Biol. Chem. 284, 22803-22814. https://doi.org/10.1074/jbc.M109.018226
- Laplante, M., and Sabatini, D. (2012). mTOR signaling in growth control and disease. Cell 149, 274-293. https://doi.org/10.1016/j.cell.2012.03.017
- Lembo, A., Di Cunto, F., and Provero, P. (2012). Shortening of 3 UTRs correlates with poor prognosis in breast and lung cancer. PLoS One 7, e31129. https://doi.org/10.1371/journal.pone.0031129
- Li, W., You, B., Hoque, M., Zheng, D., Luo, W., Ji, Z., Park, J.Y., Gunderson, S.I., Kalsotra, A., Manley, J.L., et al. (2015). Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 11, e1005166. https://doi.org/10.1371/journal.pgen.1005166
- Licatalosi, D.D., Mele, A., Fak, J.J., Ule, J., Kayikci, M., Chi, S.W., Clark, T.A., Schweitzer, A.C., Blume, J.E., Wang, X., et al. (2008). HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464-469. https://doi.org/10.1038/nature07488
- Martin, G., Gruber, A., Keller, W., and Zavolan, M. (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, 753-763. https://doi.org/10.1016/j.celrep.2012.05.003
- Masamha, C.P., Xia, Z., Yang, J., Albrecht, T.R., Li, M., Shyu, A., Li, W., and Wagner, E.J. (2014). CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature 510, 412-416. https://doi.org/10.1038/nature13261
- Mayr, C., and Bartel, D.P. (2009). Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684. https://doi.org/10.1016/j.cell.2009.06.016
- Millevoi, S., Loulergue, C., Dettwiler, S., Karaa, S.Z., Keller, W., Antoniou, M., and Vagner, S. (2006). An interaction between U2AF 65 and CF Im links the splicing and 3ae end processing machineries. EMBO J. 25, 4854-4864. https://doi.org/10.1038/sj.emboj.7601331
- Morris, A.R., Bos, A., Diosdado, B., Rooijers, K., Elkon, R., Bolijn, A.S., Carvalho, B., Meijer, G.A., and Agami, R. (2012). Alternative cleavage and polyadenylation during colorectal cancer development. Clin. Cancer Res. 18, 5256-5266. https://doi.org/10.1158/1078-0432.CCR-12-0543
- Proudfoot, N.J. (2011). Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770-1782. https://doi.org/10.1101/gad.17268411
- Sandberg, R., Neilson, J., Sarma, A., Sharp, P., and Burge, C. (2008a). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science (New York, N.Y.) 320, 1643-1647. https://doi.org/10.1126/science.1155390
- Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A., and Burge, C.B. (2008b). Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320, 1643-1647. https://doi.org/10.1126/science.1155390
- Singh, P., Alley, T.L., Wright, S.M., Kamdar, S., Schott, W., Wilpan, R.Y., Mills, K.D., and Graber, J.H. (2009). Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. Cancer Res. 69, 9422-9430. https://doi.org/10.1158/0008-5472.CAN-09-2236
- Takagaki, Y., Seipelt, R.L., Peterson, M.L., and Manley, J.L. (1996). The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell 87, 941-952. https://doi.org/10.1016/S0092-8674(00)82000-0
- Tian, B., and Manley, J.L. (2013). Alternative cleavage and polyadenylation: the long and short of it. Trends Biochem. Sci. 38, 312-320. https://doi.org/10.1016/j.tibs.2013.03.005
- Wang, E., Cody, N.L., Jog, S., Biancolella, M., Wang, T., Treacy, D., Luo, S., Schroth, G., Housman, D., Reddy, S., et al. (2012). Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150, 710-724. https://doi.org/10.1016/j.cell.2012.06.041
- Yang, Q., Gilmartin, G.M., and Doublie, S. (2010). Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3' processing. Proc. Natl. Acad. Sci. USA 107, 10062-10067. https://doi.org/10.1073/pnas.1000848107
- Yao, C., Biesinger, J., Wan, J., Weng, L., Xing, Y., Xie, X., and Shi, Y. (2012). Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc. Natl. Acad. Sci. USA 109, 18773-18778. https://doi.org/10.1073/pnas.1211101109
- Zhang, H., Lee, J., and Tian, B. (2005). Biased alternative polyadenylation in human tissues. Genome Biol. 6, R100. https://doi.org/10.1186/gb-2005-6-12-r100
- Zhang, X., Virtanen, A., and Kleiman, F.E. (2010). To polyadenylate or to deadenylate: That is the question. Cell Cycle 9, 4437-4449. https://doi.org/10.4161/cc.9.22.13887
- Zhu, H., Zhou, H., Hasman, R.A., and Lou, H. (2007). Hu proteins regulate polyadenylation by blocking sites containing U-rich sequences. J. Biol. Chem. 282, 2203-2210. https://doi.org/10.1074/jbc.M609349200
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