مروری بر نقش بیولوژیک RNAهای طویل غیرکدکننده (LncRNA) در غلات و گیاهان زراعی

نوع مقاله : مروری

نویسندگان

1 بخش بیوتکنولوژی گیاهی، دانشکده کشاورزی، دانشگاه شیراز، شیراز، ایران.

2 بخش تحقیقات زراعی و باغی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان کرمانشاه، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرمانشاه، ایران.

چکیده

بر اساس مطالعات انجام شده روی ارگانیسم‌های مختلف گیاهی، حدود 90 درصد از کل ژنوم یک ارگانیسم زنده به صورت RNA رونویسی می­شود. با این حال، تنها یک تا دو درصد از ژنوم رونویسی شده، مربوط به RNAهای کدکننده پروتئین هستند. RNAهای غیر کدکننده، مولکول‌های RNAیی هستند که الگوی ساخت هیچ پروتئینی نبوده و به اصطلاح، قابل ترجمه نیستند. RNAهای طویل غیر کد­کننده (LncRNAs) نیز دسته­ای از این RNAهای غیر کد­کننده هستند که دارای طولی بیش از 200 نوکلئوتید می‌باشند. بر اساس ارگانیسم مورد مطالعه و زمینه ژنومی، LncRNAs متنوع هستند و دارای انواع مختلفی می­باشند. از جمله انواع متفاوت این RNAها می­توان به LncRNAهای سنس (معنی) و آنتی­سنس (غیرمعنی)، اینترونیک، بین ژنی، دو طرفه و تقویت کننده اشاره کرد. LncRNAها در درجه اول با RNAهای پیام‌رسان، DNA، پروتئین و RNAهای کوچک از نظر طولی تعامل و اثرمتقابل دارند که این موضوع باعث تأثیرگذاری آن­ها روی بیان ژن‌ها در سطوح اپی‌ژنتیک، رونویسی، پس از رونویسی، ترجمه و پس از ترجمه شده و به روش­های گوناگون، زمان و مقدار بیان ژن‌ها در غلات را تحت شرایط متغیر تنظیم می­کنند. علاوه بر آن، این دسته بزرگ از RNAها، دارای نقش­های مهمی در فرآیندهای بیولوژیکی مانند بازآرایی کروماتین، فعال‌سازی رونویسی و تنظیمات پروموتوری، تداخل رونویسی به صورت اعمال توقف یا ادامه‌دار بودن آن، پردازش RNAهای رونویسی شده و کمک به ایجاد ساختار صحیح آن‌ها و همچنین ترجمه mRNA به پروتئین را در غلات و گیاهان زراعی دارند. از جمله اثرات بیولوژیکی RNAهای بلند غیر کدکننده می‌توان به نقش اساسی آن‌ها در عملکردهای مهمی مانند رشد و نمو، پاسخ به تنش‌های زنده و غیر زنده (تنش‌های محیطی)، تنظیم تمایز سلولی و چرخه سلولی در گیاهان زراعی و به ویژه غلات نام برد. با توجه به اهمیت بسیار زیاد RNAهای غیر کد­کننده خصوصاً LncRNAها و طبیعت بسیار جدید و ناشناخته بودن آن‌ها، در این مقاله مروری، به بررسی انواع و مکانیسم­های عملکرد LncRNAها در سطوح مختلف اپی ژنتیک، رونویسی، پس از رونویسی، ترجمه و پس از ترجمه در غلات و سایر گیاهان زراعی پرداخته خواهد شد. همچنین در این مقاله سعی گردیده است که ارتباط LncRNAها با پاسخ این گیاهان به تغیرات شرایط محیطی و نقش تعاملی آن‌ها روی عوامل و پروتئین­های دخیل در فعالیت‌های بیولوژیک گیاهان مورد بررسی و تحقیق قرار گیرد تا به بررسی کارهای انجام شده در داخل و خارج کشور پرداخت. خاطر نشان می‌گردد که در دنیا تعداد کمی مقالات در ارتباط با نقش و کارکرد LncRNAها به ویژه در زبان فارسی در دسترس است.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

A review on biological roles of long non-coding RNAs (LncRNAs) in plants: A focus on cereal crops

نویسندگان [English]

  • Fatemeh Sohrabi 1
  • Armin Saed-Moucheshi 2
1 Depratment of Plant Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran.
2 Crop and Horticulture Reseach Department, Kermanshah Agricultural and Natural Resources Research and Education Center (AREEO), Kermanshah, Iran.
چکیده [English]

According to the studies conducted on different plant species, about 90% of the entire genome of a plant is transcribed as RNA. However, only 1-2% of the transcribed genome is protein-coding RNAs which their transcription would end up in, at least, a protein peptide. Non-coding RNAs are RNA molecules from which no protein is synthesized and cannot be translated. Long non-coding RNAs (LncRNAs) are also a group of non-coding RNAs having a length of about 200 nucleotides. Different studies have verified that LncRNAs are widely diverse in type and function. Accordingly, sense and antisense, intronic, intergenic, bidirectional, and enhancer LncRNAs are some known altered types of LncRNAs. Long non-coding RNAa primarily interact with messenger RNAs (mRNA), DNA, proteins, and small RNAs (e.g. microRNAs, miRNA and siRNA) making them an important agent in gene expression processes at epigenetic, transcription, post-transcription, translation and post-translation-levels. There are also some studies vertifying the involvement of such RNAs in the regulatation of the time and quantity of expression in response to various conditions. In addition, this large group of RNAs has important roles in biological processes such as chromatin rearrangement, transcription activation and promoter settings, interference with the strcuture arrangement of transcriptional productions, and the mRNA-to-protein translation process. Among the biological effects of long non-coding RNAs, their essential role in phenotyping functions such as growth and development, response to biotic and abiotic stresses (environmental stresses), regulation of crop cell differentiation and cell cycle specially cereals can be mentioned. Due to the great importance of non-coding RNAs, especially LncRNAs, in this review article we try to investigate the types and mechanisms of LncRNA functions at different epigenetic, transcriptional, post-transcriptional, translational and post-transcriptional levels. Correspondingly, the relationship between LncRNAs and the response of crops to changes in environmental conditions and their interactive role on factors and proteins involved in such biological activities in crops are investigated. It has been verified that there are fewer published articles available related to the role and function of LncRNAs in biological systems of crops, especially cereal.

کلیدواژه‌ها [English]

  • chromatin rearrangement
  • gene expression regulation
  • non-coding RNA
  • post-translational
  • epigenetics
  • pre-transcriptional

مراجع

Anderson, D. M., Anderson, K. M., Chang, C.-L., Makarewich, C. A., Nelson, B. R., McAnally, J. R., Kasaragod, P., Shelton, J. M., Liou, J., & Bassel-Duby, R. 2015. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160, 595-606.
Ariel, F., Romero-Barrios, N., Jégu, T., Benhamed, M., & Crespi, M. 2015. Battles and hijacks: noncoding transcription in plants. Trends in plant science 20, 362-371.
Bari, R., Datt Pant, B., Stitt, M., & Scheible, W.-R. 2006. PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant physiology 141, 988-999.
Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. cell 116, 281-297.
Bhogireddy, S., Mangrauthia, S. K., Kumar, R., Pandey, A. K., Singh, S., Jain, A., Budak, H., Varshney, R. K., & Kudapa, H. 2021. Regulatory non-coding RNAs: a new frontier in regulation of plant biology. Functional & Integrative Genomics 21, 313-330.
Böhmdorfer, G., Rowley, M. J., Kuciński, J., Zhu, Y., Amies, I., & Wierzbicki, A. T. 2014. RNA‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA. The Plant Journal 79, 181-191.
Bond, A., Row, P., & Dudley, E. 2011. Post-translation modification of proteins; methodologies and applications in plant sciences. Phytochemistry 72, 975-996.
Bravo-Vázquez, L. A., Méndez-García, A., Chamu-García, V., Rodríguez, A. L., Bandyopadhyay, A., & Paul, S. 2024. The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research. Planta 259, 1-21.
Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A., & Rinn, J. L. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & development 25, 1915-1927.
Chekanova, J. A. 2015. Long non-coding RNAs and their functions in plants. Current opinion in plant biology 27, 207-216.
Chordia, S., Bhamwani, N., Gupta, M., Sharma, N., & Sharma, R. 2024. Machine Learning Approaches for Long Non-Coding RNA Identification in Plants. In "Non-Coding RNAs" (R. Sharma, ed.), pp. 197-214. CRC Press.
Crespi, M., Jurkevitch, E., Poiret, M., d'Aubenton‐Carafa, Y., Petrovics, G., Kondorosi, E., & Kondorosi, A. 1994. enod40, a gene expressed during nodule organogenesis, codes for a non‐translatable RNA involved in plant growth. The EMBO journal 13, 5099-5112.
Daxinger, L., Kanno, T., Bucher, E., Van Der Winden, J., Naumann, U., Matzke, A. J., & Matzke, M. 2009. A stepwise pathway for biogenesis of 24‐nt secondary siRNAs and spreading of DNA methylation. The EMBO journal 28, 48-57.
Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., & Knowles, D. G. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research 22, 1775-1789.
Devaux, Y., Zangrando, J., Schroen, B., Creemers, E., Pedrazzini, T., Chang, C., Dorn 2nd, G., Thum, T., & Heymans, S. 2015. Cardiolinc Network. Long noncoding RNAs in cardiac development and ageing. Nat. Rev. Cardiol 12, 415-425.
Dey, M., Complainville, A., Charon, C., Torrizo, L., Kondorosi, A., Crespi, M., & Datta, S. 2004. Phytohormonal responses in enod40‐overexpressing plants of Medicago truncatula and rice. Physiologia plantarum 120, 132-139.
Ding, J., Lu, Q., Ouyang, Y., Mao, H., Zhang, P., Yao, J., Xu, C., Li, X., Xiao, J., & Zhang, Q. 2012. A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proceedings of the National Academy of Sciences 109, 2654-2659.
Feng, J., Bi, C., Clark, B. S., Mady, R., Shah, P., & Kohtz, J. D. 2006. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes & development 20, 1470-1484.
Fok, E. T., Scholefield, J., Fanucchi, S., & Mhlanga, M. M. 2017. The emerging molecular biology toolbox for the study of long noncoding RNA biology. Epigenomics 9, 1317-1327.
Gelaw, T. A., & Sanan-Mishra, N. 2021. Non-coding RNAs in response to drought stress. International journal of molecular sciences 22, 12519-12534.
Gong, C., & Maquat, L. E. 2011. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470, 284-288.
Heo, J. B., & Sung, S. 2011. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76-79.
Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., & Rabani, M. 2010. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419.
Jain, A. K., Xi, Y., McCarthy, R., Allton, K., Akdemir, K. C., Patel, L. R., Aronow, B., Lin, C., Li, W., & Yang, L. 2016. LncPRESS1 is a p53-regulated LncRNA that safeguards pluripotency by disrupting SIRT6-mediated de-acetylation of histone H3K56. Molecular cell 64, 967-981.
Jha, U. C., Nayyar, H., Jha, R., Khurshid, M., Zhou, M., Mantri, N., & Siddique, K. H. 2020. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC Plant Biology 20, 1-20.
Johnson, C., Kasprzewska, A., Tennessen, K., Fernandes, J., Nan, G.-L., Walbot, V., Sundaresan, V., Vance, V., & Bowman, L. H. 2009. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome research 19, 1429-1440.
Karakülah, G., Yücebilgili Kurtoğlu, K., & Unver, T. 2016. PeTMbase: a database of plant endogenous target mimics (eTMs). PloS one 11, e0167698.
Karlik, E., Ari, S., & Gozukirmizi, N. 2019. LncRNAs: genetic and epigenetic effects in plants. Biotechnology & Biotechnological Equipment 33, 429-439.
Keniry, A., Oxley, D., Monnier, P., Kyba, M., Dandolo, L., Smits, G., & Reik, W. 2012. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nature cell biology 14, 659-665.
Keren, H., Lev-Maor, G., & Ast, G. 2010. Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics 11, 345-355.
Liu, J., Wang, H., & Chua, N. H. 2015. Long noncoding RNA transcriptome of plants. Plant biotechnology journal 13, 319-328.
Liu, N., Parisien, M., Dai, Q., Zheng, G., He, C., & Pan, T. 2013. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. Rna 19, 1848-1856.
Lubas, M., Andersen, P. R., Schein, A., Dziembowski, A., Kudla, G., & Jensen, T. H. 2015. The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. Cell reports 10, 178-192.
Magar, N. D., Shah, P., Barbadikar, K. M., Bosamia, T. C., Madhav, M. S., Mangrauthia, S. K., Pandey, M. K., Sharma, S., Shanker, A. K., & Neeraja, C. N. 2023. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. Plant Physiology and Biochemistry 13, 108-125.
Moseley, M. L., Zu, T., Ikeda, Y., Gao, W., Mosemiller, A. K., Daughters, R. S., Chen, G., Weatherspoon, M. R., Clark, H. B., & Ebner, T. J. 2006. Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8. Nature genetics 38, 758-769.
Nejat, N., & Mantri, N. 2018. Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses. Critical reviews in biotechnology 38, 93-105.
Pachnis, V., Belayew, A., & Tilghman, S. M. 1984. Locus unlinked to alpha-fetoprotein under the control of the murine raf and Rif genes. Proceedings of the National Academy of Sciences 81, 5523-5527.
Patra, G. K., Gupta, D., Rout, G. R., & Panda, S. K. 2023. Role of long non coding RNA in plants under abiotic and biotic stresses. Plant Physiology and Biochemistry 194, 96-110.
Peng, Y., Pan, R., Liu, Y., Medison, M. B., Shalmani, A., Yang, X., & Zhang, W. 2022. LncRNA‐mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato. Physiologia Plantarum 174, e13826.
Quan, M., Chen, J., & Zhang, D. 2015. Exploring the secrets of long noncoding RNAs. International journal of molecular sciences 16, 5467-5496.
Röhrig, H., Schmidt, J., Miklashevichs, E., Schell, J., & John, M. 2002. Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proceedings of the National Academy of Sciences 99, 1915-1920.
Saed-Moucheshi, A., Sohrabi, F., Fasihfar, E., Baniasadi, F., Riasat, M., & Mozafari, A. A. 2021. Superoxide dismutase (SOD) as a selection criterion for triticale grain yield under drought stress: a comprehensive study on genomics and expression profiling, bioinformatics, heritability, and phenotypic variability. BMC plant biology 21, 1-19.
Samarfard, S., Ghorbani, A., Karbanowicz, T. P., Lim, Z. X., Saedi, M., Fariborzi, N., McTaggart, A. R., & Izadpanah, K. 2022. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. Journal of Biotechnology 12, 123-138.
Seo, J. S., Sun, H.-X., Park, B. S., Huang, C.-H., Yeh, S.-D., Jung, C., & Chua, N.-H. 2017. ELF18-INDUCED LONG-NONCODING RNA associates with mediator to enhance expression of innate immune response genes in Arabidopsis. The Plant Cell 29, 1024-1038.
Song, J.-H., Cao, J.-S., & Wang, C.-G. 2013. BcMF11, a novel non-coding RNA gene from Brassica campestris, is required for pollen development and male fertility. Plant cell reports 32, 21-30.
Sun, T.-T., He, J., Liang, Q., Ren, L.-L., Yan, T.-T., Yu, T.-C., Tang, J.-Y., Bao, Y.-J., Hu, Y., & Lin, Y. 2016. LncRNA GClnc1 promotes gastric carcinogenesis and may act as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification pattern. Cancer discovery 6, 784-801.
Thomson, D. W., & Dinger, M. E. 2016. Endogenous microRNA sponges: evidence and controversy. Nature Reviews Genetics 17, 272-283.
Tseng, K.-C., Wu, N.-Y., Chow, C.-N., Zheng, H.-Q., Chou, C.-Y., Yang, C.-W., Wang, M.-J., Chang, S.-B., & Chang, W.-C. 2023. JustRNA: a database of plant long noncoding RNA expression profiles and functional network. Journal of experimental botany 74, 4949-4958.
Wang, H., Chung, P. J., Liu, J., Jang, I.-C., Kean, M. J., Xu, J., & Chua, N.-H. 2014a. Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis. Genome research 24, 444-453.
Wang, Y., Fan, X., Lin, F., He, G., Terzaghi, W., Zhu, D., & Deng, X. W. 2014b. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proceedings of the National Academy of Sciences 111, 10359-10364.
Wang, Z., Cui, Q., Su, C., Zhao, S., Wang, R., Wang, Z., Meng, J., & Luan, Y. 2023. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. International Journal of Biological Macromolecules 23, 124-142.
Waseem, M., Yang, X., Aslam, M. M., Li, M., Zhu, L., Chen, S., Li, Y., & Liu, P. 2022. Genome-wide identification of long non-coding RNAs in two contrasting rapeseed (Brassica napus L.) genotypes subjected to cold stress. Environmental and Experimental Botany 201, 104969.
Wierzbicki, A. T., Haag, J. R., & 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.
Wu, L., Liu, S., Qi, H., Cai, H., & Xu, M. 2020. Research progress on plant long non-coding RNA. Plants 9, 408.
Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D., Zilberman, D., Jacobsen, S. E., & Carrington, J. C. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS biology 2, e104.
Yoon, J.-H., Abdelmohsen, K., Kim, J., Yang, X., Martindale, J. L., Tominaga-Yamanaka, K., White, E. J., Orjalo, A. V., Rinn, J. L., & Kreft, S. G. 2013. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nature communications 4, 2939.
You, J., Zhang, Y., Liu, A., Li, D., Wang, X., Dossa, K., Zhou, R., Yu, J., Zhang, Y., & Wang, L. 2019. Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress. BMC plant biology 19, 1-16.
Zhang, H., & Zhu, J.-K. 2011. RNA-directed DNA methylation. Current opinion in plant biology 14, 142-147.
Zhang, K., Shi, Z.-M., Chang, Y.-N., Hu, Z.-M., Qi, H.-X., & Hong, W. 2014. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene 547, 1-9.
Zhao, L., Wang, J., Li, Y., Song, T., Wu, Y., Fang, S., Bu, D., Li, H., Sun, L., & Pei, D. 2021. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic acids research 49, D165-D171.
Zhao, Y., Hu, X., Liu, Y., Dong, S., Wen, Z., He, W., Zhang, S., Huang, Q., & Shi, M. 2017. ROS signaling under metabolic stress: cross-talk between AMPK and AKT pathway. Molecular cancer 16, 1-12.

فایل ها

هم رسانی

ارجاع به این مقاله

آمار