Alternative Splicing Landscape in Rice: Comparison
View Latest Version
Please note this is a comparison between Version 2 by Camila Xu and Version 1 by A.S.N.. Reddy.

Alternative splicing (AS) is a vital post-transcriptional modulator of gene expression that amplifies the proteome diversity and regulates many physiological processes essential for mounting responses to stresses in plants.

  • Alternative splicing
  • abiotic stress
  • biotic stress
Please wait, diff process is still running!

References

  1. Bhandari, H.; Mishra, A.K. Impact of demographic transformation on future rice farming in Asia. Outlook Agric. 2018, 47, 125–132.
  2. FAO. Crop Prospects and Food Situation-Quarterly Global Report No. 1; FAO: Rome, Italy, 2021.
  3. Liu, W.; Wang, G.-L. Plant innate immunity in rice: A defense against pathogen infection. Natl. Sci. Rev. 2016, 3, 295–308.
  4. Ganie, S.A.; Ahammed, G.J.; Wani, S.H. Vascular plant one zinc-finger (VOZ) transcription factors: Novel regulators of abiotic stress tolerance in rice (Oryza sativa L.). Genet. Resour. Crop. Evol. 2020, 67, 799–807.
  5. Motion, G.B.; Amaro, T.M.M.M.; Kulagina, N.; Huitema, E. Nuclear processes associated with plant immunity and pathogen susceptibility. Brief. Funct. Genom. 2015, 14, 243–252.
  6. Haak, D.C.; Fukao, T.; Grene, R.; Hua, Z.; Ivanov, R.; Perrella, G.; Li, S. Multilevel regulation of abiotic stress responses in plants. Front. Plant Sci. 2017, 8, 1564.
  7. Guerra, D.; Crosatti, C.; Khoshro, H.H.; Mastrangelo, A.M.; Mica, E.; Mazzucotelli, E. Post-transcriptional and post-translational regulations of drought and heat response in plants: A spider’s web of mechanisms. Front. Plant Sci. 2015, 6, 57.
  8. Ganie, S.A. RNA chaperones: Potential candidates for engineering salt tolerance in rice. Crop. Sci. 2020, 60, 530–540.
  9. Laloum, T.; Martín, G.; Duque, P. Alternative splicing control of abiotic stress responses. Trends Plant Sci. 2018, 23, 140–150.
  10. Rigo, R.; Bazin, J.; Crespi, M.; Charon, C. Alternative splicing in the regulation of plant–microbe interactions. Plant Cell Physiol. 2019, 60, 1906–1916.
  11. Dong, C.; He, F.; Berkowitz, O.; Liu, J.; Cao, P.; Tang, M.; Shi, H.; Wang, W.; Li, Q.; Shen, Z.; et al. Alternative splicing plays a critical role in maintaining mineral nutrient homeostasis in rice (Oryza sativa). Plant Cell 2018, 30, 2267–2285.
  12. Jabre, I.; Reddy, A.S.; Kalyna, M.; Chaudhary, S.; Khokhar, W.; Byrne, L.J.; Wilson, C.M.; Syed, N.H. Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Res. 2019, 47, 2716–2726.
  13. Chaudhary, S.; Jabre, I.; Reddy, A.S.; Staiger, D.; Syed, N.H. Perspective on alternative splicing and proteome complexity in plants. Trends Plant Sci. 2019, 24, 496–506.
  14. Zalabák, D.; Ikeda, Y. First Come, First Served: Sui Generis Features of the First Intron. Plants 2020, 9, 911.
  15. Breitbart, R.E.; Andreadis, A.; Nadal-Ginard, B. Alternative splicing: A ubiquitous mechanism for the generation of multiple protein isoforms from single genes. Annu. Rev. Biochem. 1987, 56, 467–495.
  16. Reddy, A.S.N. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu. Rev. Plant Biol. 2007, 58, 267–294.
  17. Ner-Gaon, H.; Halachmi, R.; Savaldi-Goldstein, S.; Rubin, E.; Ophir, R.; Fluhr, R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 2004, 39, 877–885.
  18. Reddy, A.S.; Rogers, M.F.; Richardson, D.N.; Hamilton, M.; Ben-Hur, A. Deciphering the plant splicing code: Experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front. Plant Sci. 2012, 3, 18.
  19. Palusa, S.G.; Reddy, A.S.N. Differential recruitment of splice variants from SR pre-mRNAs to polysomes during development and in response to stresses. Plant Cell Physiol. 2015, 56, 421–427.
  20. Reddy, A.S.N.; Marquez, Y.; Kalyna, M.; Barta, A. Complexity of the alternative splicing landscape in plants. Plant Cell 2013, 25, 3657–3683.
  21. Staiger, D.; Brown, J.W.S. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 2013, 25, 3640–3656.
  22. Black, D.L. Mechanisms of alternative pre-messenger rna splicing. Annu. Rev. Biochem. 2003, 72, 291–336.
  23. Barta, A.; Kalyna, M.; Reddy, A.S.N. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell 2010, 22, 2926–2929.
  24. Reddy, A.S.N.; Huang, J.; Syed, N.H.; Ben-Hur, A.; Dong, S.; Gu, L. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem. Soc. Trans. 2020, 48, 2399–2414.
  25. Ullah, F.; Hamilton, M.; Reddy, A.S.N.; Ben-Hur, A. Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genom. 2018, 19.
  26. Wang, X.; Hu, L.; Wang, X.; Li, N.; Xu, C.; Gong, L.; Liu, B. DNA methylation affects gene alternative splicing in plants: An example from rice. Mol. Plant 2016, 9, 305–307.
  27. Pajoro, A.; Severing, E.; Angenent, G.C.; Immink, R.G. Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. Genome Biol. 2017, 18.
  28. Yu, X.; Meng, X.; Liu, Y.; Wang, X.; Wang, T.-J.; Zhang, A.; Li, N.; Qi, X.; Liu, B.; Xu, Z.-Y. The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress. Plant Cell Rep. 2018, 38, 131–145.
  29. Yan, K.; Liu, P.; Wu, C.-A.; Yang, G.-D.; Xu, R.; Guo, Q.-H.; Huang, J.-G.; Zheng, C.-C. Stress-Induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol. Cell 2012, 48, 521–531.
  30. Campo, S.; Peris-Peris, C.; Siré, C.; Moreno, A.B.; Donaire, L.; Zytnicki, M.; Notredame, C.; Llave, C.; San Segundo, B. Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. New Phytol. 2013, 199, 212–227.
  31. Jia, F.; Rock, C.D. MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis. Plant Mol. Biol. 2013, 81, 447–460.
  32. Meng, Y.; Shao, C.; Ma, X.; Wang, H. Introns targeted by plant microRNAs: A possible novel mechanism of gene regulation. Rice 2013, 6.
  33. Park, S.-Y.; Grabau, E. Bypassing miRNA-mediated gene regulation under drought stress: Alternative splicing affects CSD1 gene expression. Plant Mol. Biol. 2017, 95, 243–252.
  34. Zhang, Y.; Rahmani, R.S.; Yang, X.; Chen, J.; Shi, T. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC Genom. 2020, 21, 1–13.
  35. Chen, L.; Tovar-Corona, J.M.; Urrutia, A.O. Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome. Int. J. Evol. Biol. 2012, 2012, 1–10.
  36. Brogna, S.; McLeod, T.; Petric, M. The meaning of NMD: Translate or perish. Trends Genet. 2016, 32, 395–407.
  37. Ohtani, M.; Wachter, A. NMD-based gene regulation—A strategy for fitness enhancement in plants? Plant Cell Physiol. 2019, 60, 1953–1960.
  38. Gracz, J. Alternative splicing in plant stress response. BioTechnologia 2016, 1, 9–17.
  39. Liu, J.; Sun, N.; Liu, M.; Liu, J.; Du, B.; Wang, X.; Qi, X. An autoregulatory loop controlling Arabidopsis HsfA2 expression: Role of heat shock-induced alternative splicing. Plant Physiol. 2013, 162, 512–521.
  40. Mastrangelo, A.M.; Marone, D.; Laidò, G.; De Leonardis, A.M.; De Vita, P. Alternative splicing: Enhancing ability to cope with stress via transcriptome plasticity. Plant Sci. 2012, 185–186, 40–49.
  41. Srivastava, A.K.; Lu, Y.; Zinta, G.; Lang, Z.; Zhu, J.-K. UTR-dependent control of gene expression in plants. Trends Plant Sci. 2018, 23, 248–259.
  42. Punzo, P.; Grillo, S.; Batelli, G. Alternative splicing in plant abiotic stress responses. Biochem. Soc. Trans. 2020, 48, 2117–2126.
  43. Palusa, S.G.; Ali, G.S.; Reddy, A.S.N. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: Regulation by hormones and stresses. Plant J. 2007, 49, 1091–1107.
  44. Chaudhary, S.; Khokhar, W.; Jabre, I.; Reddy, A.S.; Byrne, L.J.; Wilson, C.M.; Syed, N.H. Alternative Splicing and Protein Diversity: Plants Versus Animals. Front. Plant Sci. 2019, 10.
  45. Chen, M.-X.; Zhang, K.-L.; Zhang, M.; Das, D.; Fang, Y.-M.; Dai, L.; Zhang, J.; Zhu, F.-Y. Alternative splicing and its regulatory role in woody plants. Tree Physiol. 2020, 40, 1475–1486.
  46. Ling, Y.; Serrano, N.; Gao, G.; Atia, M.; Mokhtar, M.; Woo, Y.H.; Bazin, J.; Veluchamy, A.; Benhamed, M.; Crespi, M.; et al. Thermopriming triggers Splicing memory in Arabidopsis. J. Exp. Bot. 2018, 69, 2659–2675.
  47. Martin, L.B.; Fei, Z.; Giovannoni, J.J.; Rose, J.K. Catalyzing plant science research with RNA-seq. Front. Plant Sci. 2013, 4.
  48. Jain, M. Next-generation sequencing technologies for gene expression profiling in plants. Brief. Funct. Genom. 2011, 11, 63–70.
  49. Takahagi, K.; Uehara-Yamaguchi, Y.; Yoshida, T.; Sakurai, T.; Shinozaki, K.; Mochida, K.; Saisho, D. Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. Sci. Rep. 2016, 6, 1–11.
  50. He, F.; Liu, Q.; Zheng, L.; Cui, Y.; Shen, Z.; Zheng, L. RNA-seq analysis of rice roots reveals the involvement of post-transcriptional regulation in response to cadmium stress. Front. Plant Sci. 2015, 6.
  51. Wei, H.; Lou, Q.; Xu, K.; Yan, M.; Xia, H.; Ma, X.; Yu, X.; Luo, L. Alternative splicing complexity contributes to genetic improvement of drought resistance in the rice maintainer HuHan2B. Sci. Rep. 2017, 7, 1–13.
  52. Li, N.; Liu, H.; Sun, J.; Zheng, H.; Wang, J.; Yang, L.; Zhao, H.; Zou, D. Transcriptome analysis of two contrasting rice cultivars during alkaline stress. Sci. Rep. 2018, 8, 1–16.
  53. Phule, A.S.; Barbadikar, K.M.; Maganti, S.M.; Seguttuvel, P.; Subrahmanyam, D.; Babu, M.B.; Kumar, P.A. RNA-seq reveals the involvement of key genes for aerobic adaptation in rice. Sci. Rep. 2019, 9, 1–10.
  54. Razzaque, S.; Elias, S.M.; Haque, T.; Biswas, S.; Jewel, G.M.; Rahman, S.; Weng, X.; Ismail, A.M.; Walia, H.; Juenger, T.E.; et al. Gene expression analysis associated with salt stress in a reciprocally crossed rice population. Sci. Rep. 2019, 9, 1–17.
  55. Liu, G.; Zha, Z.; Cai, H.; Qin, D.; Jia, H.; Liu, C.; Qiu, D.; Zhang, Z.; Wan, Z.; Yang, Y.; et al. Dynamic transcriptome analysis of anther response to heat stress during anthesis in thermotolerant rice (Oryza sativa L.). Int. J. Mol. Sci. 2020, 21, 1155.
  56. Zhang, Z.; Xiao, B. Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs. Euphytica 2018, 214.
  57. Mansuri, R.M.; Shobbar, Z.S.; Jelodar, N.B.; Ghaffari, M.R.; Nematzadeh, G.A.; Asari, S. Dissecting molecular mechanisms underlying salt tolerance in rice: A comparative transcriptional profiling of the contrasting genotypes. Rice 2019, 12.
  58. Fu, L.; Shen, Q.; Kuang, L.; Wu, D.; Zhang, G. Transcriptomic and alternative splicing analyses reveal mechanisms of the difference in salt tolerance between barley and rice. Environ. Exp. Bot. 2019, 166, 103810.
  59. Shankar, R.; Bhattacharjee, A.; Jain, M. Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci. Rep. 2016, 6, 1–15.
  60. Junior, A.T.D.; Farias, D.D.; dos Santos, R.S.; do Amaral, M.N.; Arge, L.W.P.; Oliveira, D.D.C.; de Oliveira, A.C. The quest for more tolerant rice: How high concentrations of iron affect alternative splicing? Transcr. Open Access 2015, 3.
  61. Chen, M.-X.; Zhu, F.-Y.; Wang, F.-Z.; Ye, N.-H.; Gao, B.; Chen, X.; Zhao, S.-S.; Fan, T.; Cao, Y.-Y.; Liu, T.-Y.; et al. Alternative splicing and translation play important roles in hypoxic germination in rice. J. Exp. Bot. 2019, 70, 817–833.
  62. Sampangi-Ramaiah, M.H.; Ravishankar, K.V.; Nataraja, K.N.; Uma Shaanker, R. Endophytic fungus, Fusarium sp. reduces alternative splicing events in rice plants under salinity stress. Plant Physiol. Rep. 2019, 24, 487–495.
  63. Li, Y.-F.; Zheng, Y.; Vemireddy, L.R.; Panda, S.K.; Jose, S.; Ranjan, A.; Panda, P.; Govindan, G.; Cui, J.; Wei, K.; et al. Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress. BMC Genom. 2018, 19.
  64. Ganie, S.A.; Ahammed, G.J. Dynamics of cell wall structure and related genomic resources for drought tolerance in rice. Plant Cell Rep. 2021, 40, 437–459.
  65. Ganie, S.A.; Wani, S.H.; Henry, R.; Hensel, G. Improving rice salt tolerance by precision breeding in a new era. Curr. Opin. Plant Biol. 2021, 60, 101996.
  66. Zhang, T.; Huang, L.; Wang, Y.; Wang, W.; Zhao, X.; Zhang, S.; Zhang, J.; Hu, F.; Fu, B.; Li, Z. Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing. PLoS ONE 2017, 12.
  67. Deng, Q.; Bai, L.; Dai, L.; Chen, Y.; Fang, J.; Xie, J.; Luo, X. Identification of phosphorus stress related proteins in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.) using label-free quantitative proteomic analysis. Res. Square 2020.
  68. Wei, H.; Lou, Q.; Xu, K.; Zhou, L.; Chen, S.; Chen, L.; Luo, L. Pattern of alternative splicing different associated with difference in rooting depth in rice. Plant Soil 2020, 449, 233–248.
  69. Ganie, S.A.; Molla, K.A.; Henry, R.J.; Bhat, K.V.; Mondal, T.K. Advances in understanding salt tolerance in rice. Theor. Appl. Genet. 2019, 132, 851–870.
  70. Matsukura, S.; Mizoi, J.; Yoshida, T.; Todaka, D.; Ito, Y.; Maruyama, K.; Shinozaki, K.; Yamaguchi-Shinozaki, K. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Mol. Genet. Genom. 2010, 283, 185–196.
  71. Magaraggia, F.; Solinas, G.; Valle, G.; Giovinazzo, G.; Coraggio, I. Maturation and translation mechanisms involved in the expression of a myb gene of rice. Plant Mol. Biol. 1997, 35, 1003–1008.
  72. Cheng, Q.; Zhou, Y.; Liu, Z.; Zhang, L.; Song, G.; Guo, Z.; Wang, W.; Qu, X.; Zhu, Y.; Yang, D. An alternatively spliced heat shock transcription factor, OsHSFA2dI, functions in the heat stress-induced unfolded protein response in rice. Plant Biol. 2015, 17, 419–429.
  73. Cotsaftis, O.; Plett, D.; Shirley, N.; Tester, M.; Hrmova, M. A Two-Staged model of Na+ exclusion in rice explained by 3D modeling of HKT transporters and alternative splicing. PLoS ONE 2012, 7, e39865.
  74. Kong, J.; Gong, J.-M.; Zhang, Z.-G.; Zhang, J.-S.; Chen, S.-Y. A new AOX homologous gene OsIM1 from rice (Oryza sativa L.) with an alternative splicing mechanism under salt stress. Theor. Appl. Genet. 2003, 107, 326–331.
  75. Cordeiro, A.M.; Figueiredo, D.D.; Tepperman, J.; Borba, A.R.; Lourenço, T.; Abreu, I.A.; Ouwerkerk, P.B.F.; Quail, P.H.; Margarida Oliveira, M.; Saibo, N.J.M. Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B. Biochim. Biophys. Acta Gene Regul. Mech. 2016, 1859, 393–404.
  76. Xu, H.; Li, X.; Zhang, H.; Wang, L.; Zhu, Z.; Gao, J.; Li, C.; Zhu, Y. High temperature inhibits the accumulation of storage materials by inducing alternative splicing of OsbZIP58 during filling stage in rice. Plant Cell Environ. 2020, 43, 1879–1896.
  77. Mimida, N.; Kitamoto, H.; Osakabe, K.; Nakashima, M.; Ito, Y.; Heyer, W.-D.; Toki, S.; Ichikawa, H. Two Alternatively Spliced Transcripts generated From OSMUS81, a Rice homolog of Yeast MUS81, are Up-Regulated by DNA-Damaging Treatments. Plant Cell Physiol. 2007, 48, 648–654.
  78. Lee, A.; Lee, S.; Jung, W.; Park, H.; Lim, B.; Kim, H.-S.; Ahn, J.; Cho, H. The OsCYP19-4 Gene Is Expressed as Multiple Alternatively Spliced Transcripts Encoding Isoforms with Distinct Cellular Localizations and PPIase Activities under Cold Stress. Int. J. Mol. Sci. 2016, 17, 1154.
  79. Li, R.; Wang, W.; Li, F.; Wang, Q.; Wang, S.; Xu, Y.; Chen, F. Response of alternative splice isoforms of OsRad9 gene from Oryza sativa to environmental stress. Z. Naturforsch. C 2017, 72, 325–334.
  80. Sripinyowanich, S.; Chamnanmanoontham, N.; Udomchalothorn, T.; Maneeprasopsuk, S.; Santawee, P.; Buaboocha, T.; Qu, L.-J.; Gu, H.; Chadchawan, S. Overexpression of a Partial fragment of the salt-responsive gene OsNUC1 enhances salt adaptation in transgenic Arabidopsis thaliana and rice (Oryza sativa L.) during salt stress. Plant Sci. 2013, 213, 67–78.
  81. Koo, S.C.; Yoon, H.W.; Kim, C.Y.; Moon, B.C.; Cheong, Y.H.; Han, H.J.; Lee, S.M.; Kang, K.Y.; Kim, M.C.; Lee, S.Y.; et al. Alternative splicing of the OsBWMK1 gene generates three transcript variants showing differential subcellular localizations. Biochem. Biophys. Res. Commun. 2007, 360, 188–193.
  82. Sakuraba, Y.; Kim, D.; Han, S.-H.; Kim, S.-H.; Piao, W.; Yanagisawa, S.; An, G.; Paek, N.-C. Multilayered regulation of membrane-bound ONAC054 is essential for abscisic acid-induced leaf senescence in rice. Plant Cell 2020, 32, 630–649.
  83. Lee, C.-Y.; Tsai, Y.-C. Light-Regulated alternative splicing of Pseudo-histidine Phosphotransfer Protein 3 in Oryza sativa. J. Plant Growth Regul. 2019, 38, 1215–1227.
  84. Yang, S.-Y.; Lu, W.-C.; Ko, S.-S.; Sun, C.-M.; Hung, J.-C.; Chiou, T.-J. Upstream open reading frame and phosphate-regulated expression of rice OsNLA1 controls phosphate transport and reproduction. Plant Physiol. 2020, 182, 393–407.
  85. Zhang, Y.-M.; Yan, Y.-S.; Wang, L.-N.; Yang, K.; Xiao, N.; Liu, Y.-F.; Fu, Y.-P.; Sun, Z.-X.; Fang, R.-X.; Chen, X.-Y. A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth. Mol. Plant 2012, 5, 63–72.
  86. Larkin, P.D.; Park, W.D. Transcript accumulation and utilization of alternate and non-consensus splice sites in rice granule-bound starch synthase are temperature-sensitive and controlled by a single-nucleotide polymorphism. Plant Mol. Biol. 1999, 40, 719–727.
  87. Amin, U.S.; Biswas, S.; Elias, S.M.; Razzaque, S.; Haque, T.; Malo, R.; Seraj, Z.I. Enhanced salt tolerance conferred by the complete 2.3 kb cDNA of the rice vacuolar Na+/H+ antiporter gene compared to 1.9 kb coding region with 5′ UTR in transgenic lines of rice. Front. Plant Sci. 2016, 7.
  88. Costanzo, S.; Jia, Y. Alternatively spliced transcripts of Pi-ta blast resistance gene in Oryza sativa. Plant Sci. 2009, 177, 468–478.
  89. Cesari, S.; Thilliez, G.; Ribot, C.; Chalvon, V.; Michel, C.; Jauneau, A.; Rivas, S.; Alaux, L.; Kanzaki, H.; Okuyama, Y.; et al. The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae effectors AVR-Pia and AVR1-CO39 by direct binding. Plant Cell 2013, 25, 1463–1481.
  90. Wang, J.; Tian, D.; Gu, K.; Yang, X.; Wang, L.; Zeng, X.; Yin, Z. Induction of Xa10-like genes in rice cultivar Nipponbare confers disease resistance to rice bacterial blight. Mol. Plant Microbe Interact. 2017, 30, 466–477.
  91. Liu, J.; Chen, X.; Liang, X.; Zhou, X.; Yang, F.; Liu, J.; He, S.Y.; Guo, Z. Alternative splicing of rice WRKY62 and WRKY76 transcription factor genes in Pathogen defense. Plant Physiol. 2016, 171, 1427–1442.
  92. Duan, L.; Xiao, W.; Xia, F.; Liu, H.; Xiao, J.; Li, X.; Wang, S. Two different transcripts of A LAMMER Kinase Gene play Opposite roles in disease resistance. Plant Physiol. 2016, 172, 1959–1972.
  93. Liu, D.; Shi, S.; Hao, Z.; Xiong, W.; Luo, M. OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice. Int. J. Mol. Sci. 2019, 20, 2360.
  94. Hu, X.; Zhang, H.; Li, G.; Yang, Y.; Zheng, Z.; Song, F. Ectopic expression of a rice protein phosphatase 2C gene OsBIPP2C2 in tobacco improves disease resistance. Plant Cell Rep. 2009, 28, 985–995.
  95. Zhang, X.-B.; Feng, B.-H.; Wang, H.-M.; Xu, X.; Shi, Y.-F.; He, Y.; Chen, Z.; Sathe, A.P.; Shi, L.; Wu, J.-L. A substitution mutation in OsPELOTA confers bacterial blight resistance by activating the salicylic acid pathway. J. Integr. Plant Biol. 2018, 60, 160–172.
  96. Feng, W.; Hongbin, W.; Bing, L.; Jinfa, W. Cloning and characterization of a novel splicing isoform of the iron-superoxide dismutase gene in rice (Oryza sativa L.). Plant Cell Rep. 2006, 24, 734–742.
  97. Stracke, R.; Favory, J.; Gruber, H.; Bartelniewoehner, L.; Bartels, S.; Binkert, M.; Ulm, R. The Arabidopsis bZIP transcription factor HY5 regulates expression of the PFG1/MYB12 gene in response to light and ultraviolet-B radiation. Plant Cell Environ. 2010, 33, 88–103.
  98. Zhao, B.; Tang, Y.; Zhang, B.; Wu, P.; Li, M.; Xu, X.; Wu, G.; Jiang, H.; Chen, Y. The Temperature-Dependent Retention of Introns in GPI8 Transcripts Contributes to a Drooping and Fragile Shoot Phenotype in Rice. Int. J. Mol. Sci. 2020, 21, 299.
  99. Das, N.; Bhattacharya, S.; Bhattacharyya, S.; Maiti, M.K. Identification of alternatively spliced transcripts of rice phytochelatin synthase 2 gene OsPCS2 involved in mitigation of cadmium and arsenic stresses. Plant Mol. Biol. 2017, 94, 167–183.
  100. Sellamuthu, G.; Jegadeeson, V.; Sajeevan, R.S.; Rajakani, R.; Parthasarathy, P.; Raju, K.; Shabala, L.; Chen, Z.-H.; Zhou, M.; Sowdhamini, R.; et al. Distinct evolutionary origins of intron retention splicing events in NHX1 antiporter transcripts relate to sequence specific distinctions in Oryza species. Front. Plant Sci. 2020, 11.
  101. Koo, S.C.; Choi, M.S.; Chun, H.J.; Park, H.C.; Kang, C.H.; Shim, S.I.; Chung, J.I.; Cheong, Y.H.; Lee, S.Y.; Yun, D.-J.; et al. Identification and characterization of alternative promoters of the rice MAP kinase gene OsBWMK1. Mol. Cells 2009, 27, 467–473.
  102. Kumar, S.; Asif, M.H.; Chakrabarty, D.; Tripathi, R.D.; Dubey, R.S.; Trivedi, P.K. Comprehensive analysis of regulatory elements of the promoters of rice sulfate transporter gene family and functional characterization of OsSul1;1 promoter under different metal stress. Plant Signal. Behav. 2015, 10.
  103. Khurana, N.; Chauhan, H.; Khurana, P. Expression analysis of A Heat-inducible, Myo-inositol-1-phosphate synthase (MIPS) gene from wheat and the alternatively spliced variants of rice and Arabidopsis. Plant Cell Rep. 2011, 31, 237–251.
  104. Kumar, S.; Asif, M.H.; Chakrabarty, D.; Tripathi, R.D.; Trivedi, P.K. Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions. Funct. Integr. Genom. 2011, 11, 259–273.
  105. Wang, H.; Bian, M.; Yang, Z.; Lin, C.; Shi, W. Preliminary functional analysis of the Isoforms of OsHsfA2a (Oryza sativa L.) generated by alternative splicing. Plant Mol. Biol. Rep. 2013, 31, 38–46.
  106. Fang, Z. Differential expression pattern of splice variants of amino acid transporter genes from rice grown under various nitrogen conditions and during development. Int. J. Agric. Biol. 2017, 19, 1246–1258.
  107. Gupta, P.; Nutan, K.K.; Singla-Pareek, S.L.; Pareek, A. Abiotic stresses cause differential regulation of alternative splice forms of GATA transcription factor in rice. Front. Plant Sci. 2017, 8.
  108. Almadanim, M.C.; Gonçalves, N.M.; Rosa, M.T.G.; Alexandre, B.M.; Cordeiro, A.M.; Rodrigues, M.; Saibo, N.J.M.; Soares, C.M.; Romão, C.V.; Oliveira, M.M.; et al. The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications. Biochim. Biophys. Acta Mol. Cell Res. 2018, 1865, 231–246.
  109. Xiong, L.; Yang, Y. Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid–inducible mitogen-activated protein kinase. Plant Cell 2003, 15, 745–759.
  110. Zeng, C.; Hamada, M. RNA-Seq analysis reveals localization-associated alternative splicing across 13 cell lines. Genes 2020, 11, 820.
  111. Lu, S.-J.; Yang, Z.-T.; Sun, L.; Sun, L.; Song, Z.-T.; Liu, J.-X. Conservation of IRE1-regulated bZIP74 mRNA unconventional splicing in rice (Oryza sativa L.) involved in ER stress responses. Mol. Plant 2012, 5, 504–514.
  112. Kornblihtt, A.R. Promoter usage and alternative splicing. Curr. Opin. Cell Biol. 2005, 17, 262–268.
  113. Lin, W.-Y.; Huang, T.-K.; Chiou, T.-J. NITROGEN limitation adaptation, a target of MicroRNA827, Mediates degradation of Plasma Membrane–Localized Phosphate transporters to Maintain Phosphate homeostasis in Arabidopsis. Plant Cell 2013, 25, 4061–4074.
  114. Tanaka, M.; Sotta, N.; Yamazumi, Y.; Yamashita, Y.; Miwa, K.; Murota, K.; Chiba, Y.; Hirai, M.Y.; Akiyama, T.; Onouchi, H.; et al. The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation. Plant Cell 2016, 28, 2830–2849.
  115. Zou, M.; Guan, Y.; Ren, H.; Zhang, F.; Chen, F. Characterization of alternative splicing products of bZIP transcription factors OsABI5. Biochem. Biophys. Res. Commun. 2007, 360, 307–313.
  116. Rosa, M.T.; Almeida, D.M.; Pires, I.S.; da Rosa Farias, D.; Martins, A.G.; da Maia, L.C.; de Oliveira, A.C.; Saibo, N.J.; Oliveira, M.M.; Abreu, I.A. Insights into the transcriptional And Post-transcriptional regulation of the rice SUMOylation machinery and into the role of two rice SUMO proteases. BMC Plant Biol. 2018, 18.
  117. Hou, X.; Xie, K.; Yao, J.; Qi, Z.; Xiong, L. A homolog of human ski-interacting protein in rice positively regulates cell viability and stress tolerance. Proc. Natl. Acad. Sci. USA 2009, 106, 6410–6415.
  118. Zhang, P.; Deng, H.; Xiao, F.; Liu, Y. Alterations of Alternative Splicing Patterns of Ser/Arg-Rich (SR) Genes in Response to Hormones and Stresses Treatments in Different Ecotypes of Rice (Oryza sativa). J. Integr. Agric. 2013, 12, 737–748.
  119. Kababji, A.M. Targeted Mutagenesis and Functional Analysis of CWC25 Splicing Factor in Rice via CRISPR/Cas9. Ph.D. Thesis, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, 2019.
  120. Park, H.J.; You, Y.N.; Lee, A.; Jung, H.; Jo, S.H.; Oh, N.; Kim, H.S.; Lee, H.J.; Kim, J.K.; Kim, Y.S.; et al. OsFKBP20-1b interacts with the splicing factor OsSR45 and participates in the environmental stress response at the post-transcriptional level in rice. Plant J. 2020, 102, 992–1007.
  121. Zhang, P.; Li, S.; Chen, M. Characterization and function of circular RNAs in plants. Front. Mol. Biosci. 2020, 7.
  122. Ye, C.Y.; Chen, L.; Liu, C.; Zhu, Q.H.; Fan, L. Widespread noncoding circular RNAs in plants. New Phytol. 2015, 208, 88–95.
  123. Wang, K.; Wang, C.; Guo, B.; Song, K.; Shi, C.; Jiang, X.; Wang, K.; Tan, Y.; Wang, L.; Wang, L.; et al. CropCircDB: A comprehensive circular RNA resource for crops in response to abiotic stress. Database 2019, 2019.
  124. Wang, H.; Wang, H.; Zhang, H.; Liu, S.; Wang, Y.; Gao, Y.; Xi, F.; Zhao, L.; Liu, B.; Reddy, A.S.; et al. The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics 2019, 35, 3119–3126.
  125. Schneider, T.; Bindereif, A. Circular RNAs: Coding or noncoding? Cell Res. 2017, 27, 724–725.
  126. Wang, Y.; Wang, H.; Xi, F.; Wang, H.; Han, X.; Wei, W.; Zhang, H.; Zhang, Q.; Zheng, Y.; Zhu, Q.; et al. Profiling of circular RNA N6 -methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing. J. Integr. Plant Biol. 2020, 62, 1823–1838.
  127. Richardson, D.N.; Rogers, M.F.; Labadorf, A.; Ben-Hur, A.; Guo, H.; Paterson, A.H.; Reddy, A.S. Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing. PLoS ONE 2011, 6.
  128. Lu, C.-A.; Huang, C.-K.; Huang, W.-S.; Huang, T.-S.; Liu, H.-Y.; Chen, Y.-F. DEAD-Box RNA Helicase 42 plays a critical role in pre-mRNA splicing under cold stress. Plant Physiol. 2020, 182, 255–271.
  129. Butt, H.; Piatek, A.; Li, L.; Reddy, A.S.N.; Mahfouz, M.M. Multiplex CRISPR mutagenesis of the Serine/arginine-rich (SR) gene family in rice. Genes 2019, 10, 596.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/)
ScholarVision Creations
Feedback