Hunt, AG. Messenger RNA 3′ end formation in plants. Curr Top Microbiol Immunol 2008, 326:151–177.
Lutz, CS. Alternative polyadenylation: a twist on mRNA 3′ end formation. ACS Chem Biol 2008, 3:609–617.
Millevoi, S, Vagner, S. Molecular mechanisms of eukaryotic pre‐mRNA 3′ end processing regulation. Nucleic Acids Res 2009, 38:2757–2774.
Zhao, J, Hyman, L, Moore, C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999, 63:405–445.
Mayr, C, Bartel, DP. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009, 138:673–684.
Tollervey, D. Molecular biology: termination by torpedo. Nature 2004, 432:456–457.
Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr Opin Cell Biol 2004, 16:272–278.
Tian, B, Pan, Z, Lee, JY. Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res 2007, 17:156–165.
Macknight, R, Duroux, M, Laurie, R, Dijkwel, P, Simpson, G, Dean, C. Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA. Plant Cell 2002, 14:877–888.
Delaney, K, Xu, R, Li, QQ, Yun, KY, Falcone, DL, Hunt, AG. Calmodulin interacts with and regulates the RNA‐binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol 2006, 140:1507–1521.
Shcherbik, N, Wang, M, Lapik, YR, Srivastava, L, Pestov, DG. Polyadenylation and degradation of incomplete RNA polymerase I transcripts in mammalian cells. EMBO Rep 2010, 11:106–111.
Schuster, G, Stern, D. RNA polyadenylation and decay in mitochondria and chloroplasts. Prog Mol Biol Transl Sci 2009, 85:393–422.
Lange, H, Sement, FM, Canaday, J, Gagliardi, D. Polyadenylation‐assisted RNA degradation processes in plants. Trends Plant Sci 2009, 14:497–504.
Licatalosi, DD, Darnell, RB. RNA processing and its regulation: global insights into biological networks. Nat Rev Genet 2010, 11:75–87.
Tian, B, Hu, J, Zhang, HB, Lutz, CS. A large‐scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005, 33:201–212.
Ji, Z, Lee, JY, 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 U S A 2009, 106:7028–7033.
Singh, P, Alley, TL, Wright, SM, Kamdar, S, Schott, W, Wilpan RY, Mills KD, Graber JH. Global changes in processing of mRNA 3′ untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 2009, 69:9422–9430.
Liu, DL, Brockman, JM, Dass, B, Hutchins, LN, Singh, P, McCarrey JR, MacDonald CC, Graber JH. Systematic variation in mRNA 3′‐processing signals during mouse spermatogenesis. Nucleic Acids Res 2007, 35:234–246.
Hall‐Pogar, T, Zhang, H, Tian, B, Lutz, CS. Alternative polyadenylation of cyclooxygenase‐2. Nucleic Acids Res 2005, 33:2565–2579.
Smith, L, Coleman, LJ, Cummings, M, Satheesha, S, Shaw, SO, Speirs V, Hughes TA. Expression of estrogen receptor beta isoforms is regulated by transcriptional and post‐transcriptional mechanisms. Biochem J 2010, 429:283–290.
Liu, F, Marquardt, S, Lister, C, Swiezewski, S, Dean, C. Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 2010, 327:94–97.
Rosonina, E, Manley, JL. Alternative polyadenylation blooms. Dev Cell 2010, 18:172–174.
Hunt, AG, Xu, R, Addepalli, B, Rao, S, Forbes, KP, Meeks LR, Xing D, Mo M, Zhao H, Bandyopadhyay A. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein–protein interactions and gene expression profiling. BMC Genomics 2008, 9:220.
Xu, R, Zhao, H, Dinkins, RD, Cheng, X, Carberry, G, Li, QQ. The 73 kD subunit of the cleavage and polyadenylation specificity factor (CPSF) complex affects reproductive development in Arabidopsis. Plant Mol Biol 2006, 61:799–815.
Xu, RQ, Ye, XF, Li, QSQ. AtCPSF73‐II gene encoding an Arabidopsis homolog of CPSF 73 kDa subunit is critical for early embryo development. Gene 2004, 324:35–45.
Simpson, GG, Dijkwel, PP, Quesada, V, Henderson, I, Dean, C. FY is an RNA 3′ end‐processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 2003, 113:777–787.
Xing, D, Zhao, H, Xu, R, Li, QQ. Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p, regulates FCA alternative processing and promotes flowering time. Plant J 2008, 54:899–910.
Xing, D, Zhao, H, Li, QQ. Arabidopsis CLP1‐SIMILAR PROTEIN3, an ortholog of human polyadenylation factor CLP1, functions in gametophyte, embryo, and postembryonic development. Plant Physiol 2008, 148:2059–2069.
Rao, S, Dinkins, RD, Hunt, AG. Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biol 2009, 10:51.
Shen, Y, Liu, Y, Liu, L, Liang, C, Li, QQ. Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics 2008, 179:167–176.
Hunt, AG, Chu, NM, Odell, JT, Nagy, F, Chua, NH. Plant‐cells do not properly recognize animal gene polyadenylation signals. Plant Mol Biol 1987, 8:23–35.
Li, QQ, Hunt, AG. The polyadenylation of RNA in plants. Plant Physiol 1997, 115:321–325.
Loke, JC, Stahlberg, EA, Strenski, DG, Haas, BJ, Wood, PC, Li, QQ. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol 2005, 138:1457–1468.
Lu, Y, Gao, CX, Han, B. Sequence analysis of mRNA polyadenylation signals of rice genes. Chinese Sci Bull 2006, 51:1069–1077.
Shen, Y, Ji, G, Haas, BJ, Wu, X, Zheng, J, Reese GJ, Li QQ. Genome level analysis of rice mRNA 3′‐end processing signals and alternative polyadenylation. Nucleic Acids Res 2008, 36:3150–3161.
Graber, JH, Cantor, CR, Mohr, SC, Smith, TF. In silico detection of control signals: mRNA 3′‐end‐processing sequences in diverse species. Proc Natl Acad Sci U S A 1999, 96:14055–14060.
Li, QQ, Hunt, AG. A near upstream element in a plant polyadenylation signal consists of more than six bases. Plant Mol Biol 1995, 28:927–934.
Lin, HH, Huang, LF, Su, HC, Jeng, ST. Effects of the multiple polyadenylation signal AAUAAA on mRNA 3′‐end formation and gene expression. Planta 2009, 230:699–712.
Mogen, BD, MacDonald, MH, Graybosch, R, Hunt, AG. Upstream sequences other than AAUAAA are required for efficient messenger RNA 3′‐end formation in plants. Plant Cell 1990, 2:1261–1272.
Rothnie, HM, Reid, J, Hohn, T. The contribution of AAUAAA and the upstream element UUUGUA to the efficiency of mRNA 3′‐end formation in plants. EMBO J 1994, 13:2200–2210.
Proudfoot, N. Poly(a) signals. Cell 1991, 64:671–674.
Venkataraman, K, Brown, KM, Gilmartin, GM. Analysis of a noncanonical poly(A) site reveals a trinartite mechanism for vertebrate poly(A) site recognition. Gene Dev 2005, 19:1315–1327.
Ayliffe, MA, Steinau, M, Park, RF, Rooke, L, Pacheco, MG, Hulbert SH, Trick HN, Pryor AJ. Aberrant mRNA processing of the maize Rp1‐D rust resistance gene in wheat and barley. Mol Plant Microbe Interact 2004, 17:853–864.
Dominski, Z, Marzluff, WF. Formation of the 3′ end of histone mRNA: getting closer to the end. Gene 2007, 396:373–390.
Wodniok, S, Simon, A, Glockner, G, Becker, B. Gain and loss of polyadenylation signals during evolution of green algae. BMC Evol Biol 2007, 7:65.
Xing, A, Moon, BP, Mills, KM, Falco, SC, Li, Z. Revealing frequent alternative polyadenylation and widespread low‐level transcription read‐through of novel plant transcription terminators. Plant Biotechnol J 2010, 8:772–782.
Diehn, SH, Chiu, WL, De Rocher, EJ, Green, PJ. Premature polyadenylation at multiple sites within a Bacillus thuringiensis toxin gene‐coding region. Plant Physiol 1998, 117:1433–1443.
Koh, CH, Wong, L. Recognition of polyadenylation sites from Arabidopsis genomic sequences. Genome Inform 2007, 19:73–82.
Ji, G, Zheng, J, Shen, Y, Wu, X, Jiang, R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics 2007, 8:43.
Ji, G, Wu, X, Shen, Y, Huang, J, Wang, Z, Li, QQ. Classification‐based prediction models of messenger RNA polyadenylation sites. J Theor Biol 2010, 265:287–296.
Ji, G, Wu, X, Huang, J, Li, Q. Implementation of a classification‐based prediction model for plant mRNA poly(A) sites. J Comput Theor Nanosci 2010, 7:927–932.
Yanagisawa, S, Izui, K, Yamaguchi, Y, Shigesada, K, Katsuki, H. Further analysis of cDNA clones for maize phosphoenolpyruvate carboxylase involved in C4 photosynthesis. Nucleotide sequence of entire open reading frame and evidence for polyadenylation of mRNA at multiple sites in vivo. FEBS Lett 1988, 229:107–110.
Montoliu, L, Rigau, J, Puigdomenech, P. Multiple polyadenylation sites are active in the alpha 1‐tubulin gene from Zea mays. FEBS Lett 1990, 277:29–32.
Xu, P, Harvey, AJ, Fincher, GB. Heterologous expression of cDNAs encoding barley (Hordeum vulgare) (1–%3E3)‐beta‐glucanase isoenzyme GV. FEBS Lett 1994, 348:206–210.
Keller, T, Damude, HG, Werner, D, Doerner, P, Dixon, RA, Lamb, C. A plant homolog of the neutrophil NADPH oxidase gp91phox subunit gene encodes a plasma membrane protein with Ca2+ binding motifs. Plant Cell 1998, 10:255–266.
Cheng, Y, Kato, N, Wang, W, Li, J, Chen, X. Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre‐mRNA in Arabidopsis thaliana. Dev Cell 2003, 4:53–66.
Yoshimura, K, Yabuta, Y, Ishikawa, T, Shigeoka, S. Identification of a cis element for tissue‐specific alternative splicing of chloroplast ascorbate peroxidase pre‐mRNA in higher plants. J Biol Chem 2002, 277:40623–40632.
Tantikanjana, T, Nasrallah, ME, Stein, JC, Chen, CH, Nasrallah, JB. An alternative transcript of the S locus glycoprotein gene in a class II pollen‐recessive self‐incompatibility haplotype of Brassica oleracea encodes a membrane‐anchored protein. Plant Cell 1993, 5:657–666.
Giranton, JL, Ariza, MJ, Dumas, C, Cock, JM, Gaude, T. The S locus receptor kinase gene encodes a soluble glycoprotein corresponding to the SKR extracellular domain in Brassica oleracea. Plant J 1995, 8:827–834.
Bassett, CL, Artlip, TS, Callahan, AM. Characterization of the peach homologue of the ethylene receptor, PpETR1, reveals some unusual features regarding transcript processing. Planta 2002, 215:679–688.
Tang, G, Zhu, X, Gakiere, B, Levanony, H, Kahana, A, Galili, G. The bifunctional LKR/SDH locus of plants also encodes a highly active monofunctional lysine‐ketoglutarate reductase using a polyadenylation signal located within an intron. Plant Physiol 2002, 130:147–154.
Tang, W, Gunn, TM, McLaughlin, DF, Barsh, GS, Schlossman, SF, Duke‐Cohan, JS. Secreted and membrane attractin result from alternative splicing of the human ATRN gene. Proc Natl Acad Sci U S A 2000, 97:6025–6030.
Muralla, R, Chen, E, Sweeney, C, Gray, JA, Dickerman, A, Nikolau BJ, Meinke D. A bifunctional locus (BIO3‐BIO1) required for biotin biosynthesis in Arabidopsis. Plant Physiol 2008, 146:60–73.
Boss, PK, Bastow, RM, Mylne, JS, Dean, C. Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell 2004, 16(suppl):S18–S31.
Michaels, SD, Amasino, RM. Loss of FLOWERING LOCUS C activity eliminates the late‐flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell 2001, 13:935–941.
Simpson, GG, Quesada, V, Henderson, IR, Dijkwel, PP, Macknight, R, Dean, C. RNA processing and Arabidopsis flowering time control. Biochem Soc Trans 2004, 32:565–566.
Blazquez, MA, Ahn, JH, Weigel, D. A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nat Genet 2003, 33:168–171.
Hornyik, C, Terzi, LC, Simpson, GG. The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell 2010, 18:203–213.
Macknight, R, Bancroft, I, Page, T, Lister, C, Schmidt, R, Love K, Westphal L, Murphy G, Sherson S, Cobbett C. FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA‐binding domains. Cell 1997, 89:737–745.
Herr, AJ, Molnar, A, Jones, A, Baulcombe, DC. Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis. Proc Natl Acad Sci U S A 2006, 103:14994–15001.
Quesada, V, Macknight, R, Dean, C, Simpson, GG. Autoregulation of FCA pre‐mRNA processing controls Arabidopsis flowering time. EMBO J 2003, 22:3142–3152.
Zhao, H, Xing, D, Li, QQ. Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiol 2009, 151:1546–1556.
Henderson, IR, Liu, F, Drea, S, Simpson, GG, Dean, C. An allelic series reveals essential roles for FY in plant development in addition to flowering‐time control. Development 2005, 132:3597–3607.
Tzafrir, I, Pena‐Muralla, R, Dickerman, A, Berg, M, Rogers, R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D. Identification of genes required for embryo development in Arabidopsis. Plant Physiol 2004, 135:1206–1220.
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. 2009, 4:e8419.
Swiezewski, S, Crevillen, P, Liu, F, Ecker, JR, Jerzmanowski, A, Dean, C. Small RNA‐mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci U S A 2007, 104:3633–3638.
Zhang, J, Addepalli, B, Yun, KY, Hunt, AG, Xu, R, Rao S, Li QQ, Falcone DL. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS One 2008, 3:e2410.
Stoilov, P, Rafalska, I, Stamm, S. YTH: a new domain in nuclear proteins. Trends Biochem Sci 2002, 27:495–497.
Han, HJ, Tokino, T, Nakamura, Y. CSR, a scavenger receptor‐like protein with a protective role against cellular damage caused by UV irradiation and oxidative stress. Hum Mol Genet 1998, 7:1039–1046.
Zhu, ZH, Yu, YP, Shi, YK, Nelson, JB, Luo, JH. CSR1 induces cell death through inactivation of CPSF3. Oncogene 2009, 28:41–51.
Mellman, DL, Gonzales, ML, Song, C, Barlow, CA, Wang, P, Kendziorski C, Anderson RA. A PtdIns4,5P2‐regulated nuclear poly(A) polymerase controls expression of select mRNAs. Nature 2008, 451:1013–1017.
Liang, C, Wang, G, Liu, L, Ji, G, Liu, Y, Chen J, Webb JS, Reese G, Dean JF. WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Res 2007, 35:W137–W142.
Meyers, BC, Vu, TH, Tej, SS, Ghazal, H, Matvienko, M, Agrawal V, Ning JC, Haudenschild CD. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 2004, 22:1006–1011.
Klahre, U, Hemmingsmieszczak, M, Filipowicz, W. Extreme heterogeneity of polyadenylation sites in messenger‐RNAs encoding chloroplast RNA‐binding proteins in Nicotiana‐Plumbaginifolia. Plant Mol Biol 1995, 28:569–574.
Belostotsky, DA, Sieburth, LE. Kill the messenger: mRNA decay and plant development. Curr Opin Plant Biol 2009, 12:96–102.
Richter, JD. CPEB: a life in translation. Trends Biochem Sci 2007, 32:279–285.