RNA regulatory elements and polyadenylation in plants

Frontiers in Plant Science

Volumn 2, Issue JAN, 2012, Pages

  Hunt, Arthur G ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Alternative polyadenylation; Exons; Introns; Splicing; UTRs

Indexed keywords

EID: 84871913206     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2011.00109     Document Type: Review

References (34)

1. Allen, E., Xie, Z., Gustafson, A. M., and Carrington, J. C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207-221.
2. Borsani, O., Zhu, J., Verslues, P. E., Sunkar, R., and Zhu, J. K. (2005). Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279-1291.
3. Dean, C., Tamaki, S., Dunsmuir, P., Favreau, M., Katayama, C., Dooner, H., and Bedbrook, J. (1986). mRNA transcripts of several plant genes are polyadenylated at multiple sites in vivo. Nucleic Acids Res. 14, 2229-2240.
4. Di Giammartino, D. C., Nishida, K., and Manley, J. L. (2011). Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866.
5. Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith, R. K. Jr., Hannick, L. I., Maiti, R., Ronning, C. M., Rusch, D. B., Town, C. D., Salzberg, S. L., and White, O. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654-5666.
6. Henz, S. R., Cumbie, J. S., Kasschau, K. D., Lohmann, J. U., Carrington, J. C., Weigel, D., and Schmid, M. (2007). Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol. 144, 1247-1255.
7. Hornyik, C., Terzi, L. C., and Simpson, G. G. (2010). The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev. Cell 18, 203-213.
8. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A., and Shinozaki, K. (2004). Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res. 32, 5096-5103.
9. 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. U.S.A. 106, 7028-7033.
10. 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. doi:10.1371/journal.pone.0008419
11. Jin, H., Vacic, V., Girke, T., Lonardi, S., and Zhu, J. K. (2008). Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol. Biol. 9, 6. doi:10.1186/1471-2199-9-6
12. Kalyna, M., Lopato, S., and Barta, A. (2003). Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development. Mol. Biol. Cell 14, 3565-3577.
13. Klahre, U., Hemmings-Mieszczak, M., and Filipowicz, W. (1995). Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia. Plant Mol. Biol. 28, 569-574.
14. Lambermon, M. H., Simpson, G. G., Wieczorek Kirk, D. A., Hemmings-Mieszczak, M., Klahre, U., and Filipowicz, W. (2000). UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation. EMBO J. 19, 1638-1649.
15. Licatalosi, D. D., and Darnell, R. B. (2010). RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 11, 75-87.
16. Loke, J. C., Stahlberg, E. A., Strenski, D. G., Haas, B. J., Wood, P. C., and Li, Q. Q. (2005). Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138, 1457-1468.
17. Lopato, S., Kalyna, M., Dorner, S., Kobayashi, R., Krainer, A. R., and Barta, A. (1999). atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes. Genes Dev. 13, 987-1001.
18. Lutz, C. S., and Moreira, A. (2011). Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. Wiley Interdiscip. Rev. RNA 2, 22-31.
19. Macdonald, C. C., and McMahon, K. W. (2010). Tissue-specific mechanisms of alternative polyadenylation: testis, brain, and beyond. Wiley Interdiscip. Rev. RNA 1, 494-501.
20. Mangone, M., Manoharan, A. P., Thierry-Mieg, D., Thierry-Mieg, J., Han, T., Mackowiak, S. D., Mis, E., Zegar, C., Gutwein, M. R., Khivansara, V., Attie, O., Chen, K., Salehi-Ashtiani, K., Vidal, M., Harkins, T. T., Bouffard, P., Suzuki, Y., Sugano, S., Kohara, Y., Rajewsky, N., Piano, F., Gunsalus, K. C., and Kim, J. K. (2010). The landscape of C. elegans 3′UTRs. Science 329, 432-435.
21. 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.
22. Meyers, B. C., Vu, T. H., Tej, S. S., Ghazal, H., Matvienko, M., Agrawal, V., Ning, J., and Haudenschild, C. D. (2004). Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat. Biotechnol. 22, 1006-1011.
23. Nagasaki, H., Arita, M., Nishizawa, T., Suwa, M., and Gotoh, O. (2005). Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene 364, 53-62.
24. Raczynska, K. D., Simpson, C. G., Ciesiolka, A., Szewc, L., Lewandowska, D., McNicol, J., Szweykowska-Kulinska, Z., Brown, J. W., and Jarmolowski, A. (2010). Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res. 38, 265-278.
25. Robinson, J. T., Thorvaldsdottir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., and Mesirov, J. P. (2011). Integrative genomics viewer. Nat. Biotechnol. 29, 24-26.
26. Shen, Y., Ji, G., Haas, B. J., Wu, X., Zheng, J., Reese, G. J., and Li, Q. Q. (2008a). Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation. Nucleic Acids Res. 36, 3150-3161.
27. Shen, Y., Liu, Y., Liu, L., Liang, C., and Li, Q. Q. (2008b). Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics 179, 167-176.
28. Shen, Y., Venu, R. C., Nobuta, K., Wu, X., Notibala, V., Demirci, C., Meyers, B. C., Wang, G. L., Ji, G., and Li, Q. Q. (2011). Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res. 21, 1478-1486.
29. Shepard, P. J., Choi, E. A., Lu, J., Flanagan, L. A., Hertel, K. J., and Shi, Y. (2011). Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17, 761-772.
30. Simpson, G. G., Dijkwel, P. P., Quesada, V., Henderson, I., and Dean, C. (2003). FY is an RNA 3′ end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113, 777-787.
31. Vasudevan, S., Peltz, S. W., and Wilusz, C. J. (2002). Non-stop decay-a new mRNA surveillance pathway. Bioessays 24, 785-788.
32. Wachter, A., Tunc-Ozdemir, M., Grove, B. C., Green, P. J., Shintani, D. K., and Breaker, R. R. (2007). Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19, 3437-3450.
33. Wu, X., Liu, M., Downie, B., Liang, C., Ji, G., Li, Q. Q., and Hunt, A. G. (2011). Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Natl. Acad. Sci. U.S.A. 108, 12533-12538.
34. Zhang, H., Lee, J. Y., and Tian, B. (2005). Biased alternative polyadenylation in human tissues. Genome Biol. 6, R100.