Review
BibTex RIS Cite

Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants

Year 2025, Volume: 11 Issue: 1-2, 17 - 25, 29.12.2025

Abstract

Non-coding RNAs (ncRNAs) are molecules that play important biological roles in plant growth but lack coding capacity. They are widely distributed in all living species. The advancement of high-throughput sequencing technology (RNA-seq) has enabled the identification of various ncRNAs. Their activities and mechanisms of action have become increasingly clear. Recent studies indicate that ncRNAs are critical for plant growth, development, and responses to environmental stress. In particular, elucidating miRNA-lncRNA-circRNA interaction processes will help identify genetic adaptations in plant stress resistance. The categorization of lncRNAs, their roles, and mechanisms in plant responses to environmental challenges are briefly summarized. The functions of ncRNAs in root and leaf development, plant growth and development, dormancy, germination, and flower formation are emphasized. Long non-coding RNAs (lncRNAs) function as sponges, precursors, scaffolds, and regulatory complexes, and serve as transcription factors (TFs) and chromatin modification structures. lncRNAs serve as regulators in epigenetics and significantly influence processes such as chromatin network remodeling and DNA methylation.

References

  • BELOUSOVA, E., FİLİPENKO, M., & KUSHLİNSKİİ, N. (2018). Circular RNA: New regulatory molecules. Bulletin of Experimental Biology and Medicine, 164, 803–815.
  • BHAR, A., & ROY, A. (2023). Emphasizing the role of long non-coding RNAs (lncRNA), circular RNA (circRNA), and micropeptides (miPs) in plant biotic stress tolerance. Plants, 12(23), 3951. https://doi.org/10.3390/plants12233951
  • CHAO, H., HU, Y., ZHAO, L., XİN, S., Nİ, Q., ZHANG, P., & CHEN, M. (2022). Biogenesis, functions, interactions, and resources of non-coding RNAs in plants. International Journal of Molecular Sciences, 23(7), 3695. https://doi.org/10.3390/ijms23073695
  • DELPU, Y., LARRIEU, D., GAYRAL, M., ARVANITIS, D., DUFRESNE, M., CORDELIER, P., & TORRISANI, J. (2016). Noncoding RNAs: clinical and therapeutic applications. In Drug discovery in cancer epigenetics (pp. 305-326). Academic Press.
  • EREN, A. H., İLHAN, E., & İNAL, B. (2016). Yeni nesil dizileme teknolojisi ile bitkilerde miRNA analizi. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 26(3), 448-454.
  • FAN, J., QUAN, W. L., Lİ, G. B., HU, X. H., WANG, Q., WANG, H., ... WANG, W. M. (2020). circRNAs are involved in the rice-Magnaporthe oryzae interaction. Plant Physiology, 182, 272–286.
  • FEUERSTEİN, E., MANAVELLA, P., CRESPİ, M., FERRERO, L., & ARİEL, F. (2025). Long noncoding RNAs in plant chromatin 3D conformation dynamics. Current Opinion in Plant Biology, 88, 102817. https://doi.org/10.1016/j.pbi.2025.102817
  • GHORBANİ, A., IZADPANAH, K., PETERS, J. R., DİETZGEN, R. G., & MİTTER, N. (2018). Detection and profiling of circular RNAs in uninfected and maize Iranian mosaic virus-infected maize. Plant Science, 274, 402–409.
  • HAWKES, E. J., HENNELLY, S. P., NOVİKOVA, I. V., IRWİN, J. A., DEAN, C., & SANBONMATSU, K. Y. (2016). COOLAIR antisense RNAs form evolutionarily conserved elaborate secondary structures. Cell Reports, 16, 3087-3096. https://doi.org/10.1016/j.celrep.2016.08.045
  • JİA, Y. Q., ZHAO, H. M., NİU, Y. N., & WANG, Y. C. (2023). Identification of birch lncRNAs and mRNAs responding to salt stress and characterization of functions of lncRNA. Horticulture Research, 10, uhac277.
  • Lİ, P., YANG, H., WANG, L., LİU, H. J., HUO, H. Q., ZHANG, C. J., ... LİU, L. (2019). Physiological and transcriptome analyses reveal short-term responses and formation of memory under drought stress in rice. Frontiers in Genetics, 10, 55.
  • LİAO, X., Lİ, X.-J., ZHENG, G.-T., CHANG, F.-R., FANG, L., YU, H., ... ZHANG, Y.-F. (2022). Mitochondrion-encoded circular RNAs are widespread and translatable in plants. Plant Physiology, 189, 1482–1500.
  • LİU, F., XU, Y. R., CHANG, K. X., Lİ, S. N., LİU, Z. G., Qİ, S. D., ... WANG, Y. (2019). The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis. New Phytologist, 224, 117–131.
  • LİU, X., Lİ, D. Y., ZHANG, D. L., YİN, D. D., ZHAO, Y., Jİ, C. J., ... ZHU, L. H. (2018). A novel antisense long noncoding RNA, TWISTED LEAF, maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice. New Phytologist, 218, 774–788.
  • LU, D., ZHANG, Y., LİU, Y., Lİ, Y., ZUO, X., LİN, J., & CUİ, Y. (2024). Recent advances of non-coding RNA in plant growth, development and stress response. Chinese Bulletin of Botany, 59(5), 709-725.
  • MA, L., BAJİC, V. B., & ZHANG, Z. (2013). On the classification of long non-coding RNAs. RNA Biology, 10(6), 925-933. https://doi.org/10.4161/rna.24604
  • NADHAN, R., ISİDORO, C., SONG, Y. S., & DHANASEKARAN, D. N. (2022). Signaling by LncRNAs: Structure, cellular homeostasis, and disease pathology. Cells, 11(16), 2517. https://doi.org/10.3390/cells11162517
  • NELSON, B. R., MAKAREWİCH, C. A., ANDERSON, D. M., WİNDERS, B. R., TROUPES, C. D., ... OLSON, E. N. (2016). A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle. Science, 351, 271–275.
  • PONTİNG, C. P., OLİVER, P. L., & REİK, W. (2009). Evolution and functions of long noncoding RNAs. Cell, 136, 629–641.
  • PRALL, W., BRİAN, D., & GREGORY, K. (2022). The fold makes all the difference in COOLAIR-mediated regulation of plant flowering time. Developmental Cell. https://doi.org/10.1016/j.devcel.2022.09.008
  • QİN, T., ZHAO, H. Y., CUİ, P., ALBESHER, N., & XİONG, L. M. (2017). A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiology, 175, 1321–1336.
  • SANGER, H. L., KLOTZ, G., RIESNER, D., GROSS, H. J., & KLEINSCHMIDT, A. K. (1976). Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proceedings of the National Academy of Sciences, 73(11), 3852-3856.
  • SONG, R. J., MA, S. Q., XU, J. J., REN, X., GUO, P. L., ... Lİ, X. D. (2023). A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR. Molecular Cancer, 22, 16.
  • SWİEZEWSKİ, S., LİU, F., MAGUSİN, A., & DEAN, C. (2009). Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature, 462, 799-802.
  • TOGNACCA, R. S., & BOTTO, J. F. (2021). Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions. Plant Communications, 2, 100169.
  • TREVASKİS, B. (2010). The central role of the VERNALIZATION1 gene in the vernalization response of cereals. Functional Plant Biology, 37(6), 479-487.
  • WANG, H. V., & CHEKANOVA, J. A. (2017). Long noncoding RNAs in plants. Advances in Experimental Medicine and Biology, 1008, 133-154. https://doi.org/10.1007/978-981-10-5203-3_5
  • WANG, X. S., CHANG, X. C., JİNG, Y., ZHAO, J. L., FANG, Q. W., ... Lİ, Y. G. (2020). Identification and functional prediction of soybean circRNAs involved in low-temperature responses. Journal of Plant Physiology, 250, 153188.
  • WANG, Y. Q., FAN, Y. Y., FAN, D., ZHOU, X. L., JİAO, Y. T., ... ZHU, D. M. (2023). The noncoding RNA HIDDEN TREASURE1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis. Plant Cell, 35, 700–716.
  • WEİ, J., HUANG, K., YANG, C., & KANG, C. (2017). Non-coding RNAs as regulators in epigenetics (Review). Oncology Reports, 37(1), 3-9. https://doi.org/10.3892/or.2016.5236
  • WU, J., LİU, C. X., LİU, Z. G., Lİ, S., Lİ, D. D., ... YUKAWA, Y. (2019). Pol III-dependent cabbage BoNR8 long ncRNA affects seed germination and growth in Arabidopsis. Plant and Cell Physiology, 60, 421–435.
  • XİA, K. F., PAN, X. Q., CHEN, H. P., XU, X. L., & ZHANG, M. Y. (2023). Rice miR168a-5p regulates seed length, nitrogen allocation and salt tolerance by targeting OsOFP3, OsNPF2.4 and OsAGO1a, respectively. Journal of Plant Physiology, 280, 153905.
  • XU, S., DONG, Q., DENG, M., LİN, D., XİAO, J., CHENG, P., & CHONG, K. (2021). The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat. Molecular Plant, 14(9), 1525-1538.
  • YADAV, A., MATHAN, J., DUBEY, A. K., & SİNGH, A. (2024). The emerging role of non-coding RNAs (ncRNAs) in plant growth, development, and stress response signaling. Non-Coding RNA, 10(1), 13. https://doi.org/10.3390/ncrna10010013
  • YANG, J., ARİEL, F., & WANG, D. (2023). Plant long non-coding RNAs: Biologically relevant and mechanistically intriguing. Journal of Experimental Botany, 74, 2364-2373.
  • ZHANG, H., LANG, Z., & ZHU, J. K. (2018). Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology, 19, 489–506. https://doi.org/10.1038/s41580-018-0016-z
  • ZHANG, L. L., LİN, T., ZHU, G. N., WU, B., ZHANG, C. J., & ZHU, H. L. (2023). LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response. Horticulture Research, 10, uhad-234.
  • ZHANG, L., LİU, J. L., CHENG, J. R., SUN, Q., ZHANG, Y., ... CAİ, Y. F. (2022). lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt. Plant Physiology, 189, 264–284.
  • ZHANG, N., LİU, Z. G., SUN, S. C., LİU, S. Y., LİN, J. H., ... WU, J. (2020). Response of AtR8 lncRNA to salt stress and its regulation on seed germination in Arabidopsis. Chinese Bulletin of Botany, 55, 421–429. ZHANG, P., & DAİ, M. Q. (2022). CircRNA: A rising star in plant biology. Journal of Genetics and Genomics, 49, 1081–1092.
  • ZHANG, X. P., DONG, J., DENG, F. N., WANG, W., CHENG, Y. Y., ... SHEN, F. F. (2019). The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. BMC Plant Biology, 19, 459.
  • ZHANG, X. P., SHEN, J., XU, Q. J., DONG, J., SONG, L. R., WANG, W., & SHEN, F. F. (2021). Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton. Plant, Cell & Environment, 44, 3302–3321.
  • ZHOU, J. P., YUAN, M. Z., ZHAO, Y. X., QUAN, Q., YU, D., ... ZHANG, Y. (2021). Efficient deletion of multiple circle RNA loci by CRISPR-Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice. Plant Biotechnology Journal, 19, 1240–1252.
  • ZHOU, J., YANG, L. Y., JİA, C. L., SHİ, W. G., DENG, S. R., & LUO, Z. B. (2022). Identification and functional prediction of poplar root circRNAs involved in treatment with different forms of nitrogen. Frontiers in Plant Science, 13, 941380.
  • ZHOU, R., XU, L. P., ZHAO, L. P., WANG, Y. L., & ZHAO, T. M. (2018). Genome-wide identification of circRNAs involved in tomato fruit coloration. Biochemical and Biophysical Research Communications, 499, 466–469.
  • ZHU, Y. X., JİA, J. H., YANG, L., XİA, Y. C., ZHANG, H. L., ... LİU, L. C. (2019). Identification of cucumber circular RNAs responsive to salt stress. BMC Plant Biology, 19, 164.
There are 45 citations in total.

Details

Primary Language English
Subjects Plant Biotechnology, Plant Cell and Molecular Biology
Journal Section Review
Authors

Abdil Hakan Eren 0009-0000-0004-1732

Submission Date December 1, 2025
Acceptance Date December 18, 2025
Publication Date December 29, 2025
Published in Issue Year 2025 Volume: 11 Issue: 1-2

Cite

APA Eren, A. H. (2025). Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants. Eastern Anatolian Journal of Science, 11(1-2), 17-25.
AMA Eren AH. Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants. Eastern Anatolian Journal of Science. December 2025;11(1-2):17-25.
Chicago Eren, Abdil Hakan. “Classification and Biological Function of NcRNAs (lncRNAs and CircRNAs) in Plants”. Eastern Anatolian Journal of Science 11, no. 1-2 (December 2025): 17-25.
EndNote Eren AH (December 1, 2025) Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants. Eastern Anatolian Journal of Science 11 1-2 17–25.
IEEE A. H. Eren, “Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants”, Eastern Anatolian Journal of Science, vol. 11, no. 1-2, pp. 17–25, 2025.
ISNAD Eren, Abdil Hakan. “Classification and Biological Function of NcRNAs (lncRNAs and CircRNAs) in Plants”. Eastern Anatolian Journal of Science 11/1-2 (December2025), 17-25.
JAMA Eren AH. Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants. Eastern Anatolian Journal of Science. 2025;11:17–25.
MLA Eren, Abdil Hakan. “Classification and Biological Function of NcRNAs (lncRNAs and CircRNAs) in Plants”. Eastern Anatolian Journal of Science, vol. 11, no. 1-2, 2025, pp. 17-25.
Vancouver Eren AH. Classification and Biological Function of ncRNAs (lncRNAs and circRNAs) in Plants. Eastern Anatolian Journal of Science. 2025;11(1-2):17-25.