Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis

Frontiers in Plant Science

Volumn 6, Issue June, 2015, Pages

  Bazin, Jeremie ^a,b   Bailey Serres, Julia ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CNRS   (France)

Author keywords

Alternative splicing; Chromatin loop; Long non coding RNA; Phosphate homeostasis; RNA sequencing; Root development; Translation regulation

Indexed keywords

EID: 84935870586     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00400     Document Type: Review

References (38)

1. Ben Amor, B., Wirth, S., Merchan, F., Laporte, P., d’Aubenton-Carafa, Y., Hirsch, J., et al. (2009). Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 19, 57-69. doi: 10.1101/gr.080275.108
2. Ariel, F., Jegu, T., Latrasse, D., Romero-Barrios, N., Christ, A., Benhamed, M., et al. (2014). Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol. Cell 55, 383-396. doi: 10.1016/j.molcel.2014.06.011
3. Bardou, F., Ariel, F., Simpson, C. G., Romero-Barrios, N., Laporte, P., Balzergue, S., et al. (2014). Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev. Cell 30, 166-176. doi: 10.1016/j.devcel.2014.06.017
4. Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. doi: 10.1038/nature05874
5. Burleigh, S. H., and Harrison, M. J. (1999). The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots. Plant Physiol. 119, 241-248.
6. Campalans, A., Kondorosi, A., and Crespi, M. (2004). Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula. Plant Cell 16, 1047-1059. doi: 10.1105/tpc.019406
7. Carrieri, C., Cimatti, L., Biagioli, M., Beugnet, A., Zucchelli, S., Fedele, S., et al. (2012). Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491, 454-457. doi: 10.1038/nature11508
8. Cech, T. R., and Steitz, J. A. (2014). The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157, 77-94. doi: 10.1016/j.cell.2014.03.008
9. Deal, R. B., and Henikoff, S. (2011). The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat. Protoc. 6, 56-68. doi: 10.1038/nprot.2010.175
10. Franco-Zorrilla, J. M., Valli, A., Todesco, M., Mateos, I., Puga, M. I., Rubio-Somoza, I., et al. (2007). Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39, 1033-1037. doi: 10.1038/ng2079
11. Geisler, S., and Coller, J. (2013). RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 14, 699-712. doi: 10.1038/nrm3679
12. Van Heesch, S., van Iterson, M., Jacobi, J., Boymans, S., Essers, P. B., de Bruijn, E., et al. (2014). Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol. 15, R6. doi: 10.1186/gb-2014-15-1-r6
13. Heo, J. B., and Sung, S. (2011). Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76-79. doi: 10.1126/science.1197349
14. Huang, F., Zago, M. K., Abas, L., van Marion, A., Galván-Ampudia, C. S., and Offringa, R. (2010). Phosphorylation of conserved PIN motifs directs Arabidopsis PIN1 polarity and auxin transport. Plant Cell 22, 1129-1142. doi: 10.1105/tpc.109.072678
15. Huang, T.-K., Han, C.-L., Lin, S.-I., Chen, Y.-J., Tsai, Y.-C., Chen, Y.-R., et al. (2013). Identification of downstream components of ubiquitin-conjugating enzyme PHOSPHATE2 by quantitative membrane proteomics in Arabidopsis roots. Plant Cell 25, 4044-4060. doi: 10.1105/tpc.113.115998
16. Jabnoune, M., Secco, D., Lecampion, C., Robaglia, C., Shu, Q., and Poirier, Y. (2013). A rice cis-natural antisense RNA acts as a translational enhancer for its cognate mRNA and contributes to phosphate homeostasis and plant fitness. Plant Cell 25, 4166-4182. doi: 10.1105/tpc.113.116251
17. Jiao, Y., and Meyerowitz, E. M. (2010). Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol. Syst. Biol. 6:419. doi: 10.1038/msb.2010.76
18. Juntawong, P., Girke, T., Bazin, J., and Bailey-Serres, J. (2014). Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 111, E203-E212. doi: 10.1073/pnas.1317811111
19. Kestrel, R. and Chen, X. (2013). Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25, 2383-2399. doi: 10.1105/tpc.113.113159
20. Kim, E.-D., and Sung, S. (2012). Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci. 17, 16-21. doi: 10.1016/j.tplants.2011.10.008
21. Kim, Y. J., Zheng, B., Yu, Y., Won, S. Y., Mo, B., and Chen, X. (2011). The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J. 30, 814-822. doi: 10.1038/emboj.2011.3
22. Li, S., Vandivier, L. E., Tu, B., Gao, L., Won, S. Y., li, S., et al. (2014). Detection of Pol IV/RDR2-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis. Genome Res. 25, 235-245. doi: 10.1101/gr.182238.114
23. Liu, J., Jung, C., Xu, J., Wang, H., Deng, S., Bernad, L., et al. (2012a). Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24, 4333-4345. doi: 10.1105/tpc.112.102855
24. Liu, T.-Y., Huang, T.-K., Tseng, C.-Y., Lai, Y.-S., Lin, S.-I., Lin, W.-Y., et al. (2012b). PHO2-dependent degradation of PHO1 modulates phosphate homeostasis in Arabidopsis. Plant Cell 24, 2168-2183. doi: 10.1105/tpc.112.096636
25. Misson, J., Raghothama, K. G., Jain, A., Jouhet, J., Block, M. A., Bligny, R., et al. (2005). A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc. Natl. Acad. Sci. U.S.A. 102, 11934-11939. doi: 10.1073/pnas.0505266102
26. Mustroph, A., Zanetti, M. E., Jang, C. J. H., Holtan, H. E., Repetti, P. P., Galbraith, D. W., et al. (2009). Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 106, 18843-18848. doi: 10.1073/pnas.0906131106
27. Rinn, J. L., and Chang, H. Y. (2012). Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145-166. doi: 10.1146/annurev-biochem-051410-092902
28. Secco, D., Baumann, A., and Poirier, Y. (2010). Characterization of the rice PHO1 gene family reveals a key role for OsPHO1;2 in phosphate homeostasis and the evolution of a distinct clade in dicotyledons. Plant Physiol. 152, 1693-1704. doi: 10.1104/pp.109.149872
29. Secco, D., Jabnoune, M., Walker, H., Shou, H., Wu, P., Poirier, Y., et al. (2013). Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. Plant Cell 25, 4285-4304. doi: 10.1105/tpc.113.117325
30. Shin, H., Shin, H.-S., Chen, R., and Harrison, M. J. (2006). Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation. Plant J. 45, 712-726. doi: 10.1111/j.1365-313X.2005.02629.x
31. Sugiyama, T., Cam, H. P., Sugiyama, R., Noma, K., Zofall, M., Kobayashi, R., et al. (2007). SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128, 491-504. doi: 10.1016/j.cell.2006.12.035
32. Swiezewski, S., Liu, F., Magusin, A., and Dean, C. (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799-802. doi: 10.1038/nature08618
33. Vaughn, M. W., and Martienssen, R. A. (2005). Finding the right template: RNA Pol IV, a plant-specific RNA polymerase. Mol. Cell 17, 754-756. doi: 10.1016/j.molcel.2005.03.003
34. Wang, H., Chung, P. J., Liu, J., Jang, I.-C., Kean, M. J., Xu, J., et al. (2014). Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome Res. 24, 444-453. doi: 10.1101/gr.165555.113
35. Wierzbicki, A. T., Haag, J. R., and Pikaard, C. S. (2008). Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635-648. doi: 10.1016/j.cell.2008.09.035
36. Wu, H.-J., Wang, Z.-M., Wang, M., and Wang, X.-J. (2013). Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol. 161, 1875-1884. doi: 10.1104/pp.113.215962
37. Zanetti, M. E., Chang, I.-F., Gong, F., Galbraith, D. W., and Bailey-Serres, J. (2005). Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol. 138, 624-635. doi: 10.1104/pp.105.059477
38. Zhang, X., Henderson, I. R., Lu, C., Green, P. J., and Jacobsen, S. E. (2007). Role of RNA polymerase IV in plant small RNA metabolism. Proc. Natl. Acad. Sci. U.S.A. 104, 4536-4541. doi: 10.1073/pnas.0611456104