Regulatory Non-coding RNAs: Emerging Roles During Plant Cell Reprogramming and Regeneration

Overview

Journal Front Plant Sci

Date 2022 Nov 28

PMID 36438127

Authors

Daniela Cordeiro

Jorge Canhoto

Sandra Correia

Affiliations

Soon will be listed here.

Abstract

Plant regeneration is a well-known capacity of plants occurring either or . This potential is the basis for plant micropropagation and genetic transformation as well as a useful system to analyse different aspects of plant development. Recent studies have proven that RNA species with no protein-coding capacity are key regulators of cellular function and essential for cell reprogramming. In this review, the current knowledge on the role of several ncRNAs in plant regeneration processes is summarized, with a focus on cell fate reprogramming. Moreover, the involvement/impact of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and small-interfering RNAs (siRNAs) in the regulatory networks of cell dedifferentiation, proliferation and differentiation is also analysed. A deeper understanding of plant ncRNAs in somatic cell reprogramming will allow a better modulation of regeneration processes such as organogenesis and somatic embryogenesis.

References

Juarez-Gonzalez V, Lopez-Ruiz B, Baldrich P, Lujan-Soto E, Meyers B, Dinkova T . The explant developmental stage profoundly impacts small RNA-mediated regulation at the dedifferentiation step of maize somatic embryogenesis. Sci Rep. 2019; 9(1):14511. PMC: 6786999. DOI: 10.1038/s41598-019-50962-y. View

Kareem A, Radhakrishnan D, Sondhi Y, Aiyaz M, Roy M, Sugimoto K . De novo assembly of plant body plan: a step ahead of Deadpool. Regeneration (Oxf). 2016; 3(4):182-197. PMC: 5084358. DOI: 10.1002/reg2.68. View

Urquiaga M, Thiebaut F, Hemerly A, Ferreira P . From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress. Front Plant Sci. 2021; 11:603246. PMC: 7815527. DOI: 10.3389/fpls.2020.603246. View

Yang X, Wang L, Yuan D, Lindsey K, Zhang X . Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. J Exp Bot. 2013; 64(6):1521-36. PMC: 3617824. DOI: 10.1093/jxb/ert013. View

Guttman M, Donaghey J, Carey B, Garber M, Grenier J, Munson G . lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 2011; 477(7364):295-300. PMC: 3175327. DOI: 10.1038/nature10398. View

Dal Santo S, De Paoli E, Pagliarani C, Amato A, Celii M, Boccacci P . Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine. Plant Physiol. 2021; 188(1):490-508. PMC: 8774814. DOI: 10.1093/plphys/kiab477. View

Borges F, Martienssen R . The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol. 2015; 16(12):727-41. PMC: 4948178. DOI: 10.1038/nrm4085. View

Gao Y, Li D, Zhang L, Borthakur D, Li Q, Ye J . MicroRNAs and their targeted genes associated with phase changes of stem explants during tissue culture of tea plant. Sci Rep. 2019; 9(1):20239. PMC: 6934718. DOI: 10.1038/s41598-019-56686-3. View

Chen L, Zhang S . Long noncoding RNAs in cell differentiation and pluripotency. Cell Tissue Res. 2016; 366(3):509-521. DOI: 10.1007/s00441-016-2451-5. View

10.

Zhang J, Zhang S, Han S, Wu T, Li X, Li W . Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis. Planta. 2012; 236(2):647-57. DOI: 10.1007/s00425-012-1643-9. View

11.

Ding J, Shen J, Mao H, Xie W, Li X, Zhang Q . RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol Plant. 2012; 5(6):1210-6. DOI: 10.1093/mp/sss095. View

12.

Chen M, Penfield S . Feedback regulation of COOLAIR expression controls seed dormancy and flowering time. Science. 2018; 360(6392):1014-1017. DOI: 10.1126/science.aar7361. View

13.

Datta R, Paul S . Long non-coding RNAs: Fine-tuning the developmental responses in plants. J Biosci. 2019; 44(4). View

14.

Lopez-Ruiz B, Juarez-Gonzalez V, Gomez-Felipe A, de Folter S, Dinkova T . tasiR-ARFs Production and Target Regulation during In Vitro Maize Plant Regeneration. Plants (Basel). 2020; 9(7). PMC: 7411845. DOI: 10.3390/plants9070849. View

15.

Zhang H, Lang Z, Zhu J . Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol. 2018; 19(8):489-506. DOI: 10.1038/s41580-018-0016-z. View

16.

Ariel F, Romero-Barrios N, Jegu T, Benhamed M, Crespi M . Battles and hijacks: noncoding transcription in plants. Trends Plant Sci. 2015; 20(6):362-71. DOI: 10.1016/j.tplants.2015.03.003. View

17.

Bardou F, Ariel F, Simpson C, Romero-Barrios N, Laporte P, Balzergue S . Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Dev Cell. 2014; 30(2):166-76. DOI: 10.1016/j.devcel.2014.06.017. View

18.

Lardon R, Geelen D . Natural Variation in Plant Pluripotency and Regeneration. Plants (Basel). 2020; 9(10). PMC: 7598583. DOI: 10.3390/plants9101261. View

19.

Yu Y, Jia T, Chen X . The 'how' and 'where' of plant microRNAs. New Phytol. 2017; 216(4):1002-1017. PMC: 6040672. DOI: 10.1111/nph.14834. View

20.

Zhang X, Wang W, Zhu W, Dong J, Cheng Y, Yin Z . Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels. Int J Mol Sci. 2019; 20(22). PMC: 6888083. DOI: 10.3390/ijms20225573. View