Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation.
Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
- Jabnoune M, Secco D, Lecampion C, Robaglia C, Shu Q, 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. https://doi.org/10.1105/tpc.113.116251 CrossRefPubMedPubMedCentralGoogle Scholar
- Lisch D (2009) Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol 60:43–66. https://doi.org/10.1146/annurev.arplant.59.032607.092744 CrossRefPubMedGoogle Scholar
- Matsunaga W, Kobayashi A, Kato A, Ito H (2012) The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana. Plant Cell Physiol 53:824–833. https://doi.org/10.1093/pcp/pcr179 CrossRefPubMedGoogle Scholar
- Secco D, Baumann A, 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. https://doi.org/10.1104/pp.109.149872 CrossRefPubMedPubMedCentralGoogle Scholar
- Shin SY, Jeong JS, Lim JY, Kim T, Park JH, Kim JK, Shin C (2018) Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies. BMC Genomics 19:532. https://doi.org/10.1186/s12864-018-4897-1 CrossRefPubMedPubMedCentralGoogle Scholar
- Snyman MC, Solofoharivelo MC, Souza-Richards R, Stephan D, Murray S, Burger JT (2017) The use of high-throughput small RNA sequencing reveals differentially expressed microRNAs in response to aster yellows phytoplasma-infection in Vitis vinifera cv. ‘Chardonnay’. PloS one 12:e0182629. https://doi.org/10.1371/journal.pone.0182629 CrossRefPubMedPubMedCentralGoogle Scholar
- Sousa C, Johansson C, Charon C, Manyani H, Sautter C, Kondorosi A, Crespi M (2001) Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex. Mol Cell Biol 21:354–366. https://doi.org/10.1128/mcb.21.1.354-366.2001 CrossRefPubMedPubMedCentralGoogle Scholar
- Xin M et al (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 11:61. https://doi.org/10.1186/1471-2229-11-61 CrossRefPubMedPubMedCentralGoogle Scholar
- Zhang Y, Wang Y, Xie F, Li C, Zhang B, Nichols RL, Pan X (2016) Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing. Funct Integr Genomics 16:127–142. https://doi.org/10.1007/s10142-015-0472-x CrossRefPubMedGoogle Scholar
- Zou J et al (2011) De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. Plant J 68:212–224. https://doi.org/10.1111/j.1365-313x.2011.04679.x CrossRefPubMedGoogle Scholar