The role of long non-coding RNAs in plants

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Abstract

Long non-coding RNAs (lncRNAs) are a class of linear or circular RNA molecules longer than 200 nucleotides without open reading frames. Experimental studies have shown the involvement of lncRNAs in the regulation of resistance to cold, salt, and heat stress, and in fruit, root, and leaf development. However, experimental methods are labor-intensive and costly approaches and cannot yet be used for genome-wide mass studies of lncRNAs. For this purpose, bioinformatic approaches that aim at large-scale recognition of lncRNA sequences in genomes and transcriptomes have been applied. However, despite the growing number of studies devoted to the structural and functional analysis of lncRNAs, this type of molecule remains poorly understood. This is due to the many factors that need to be considered when identifying lncRNAs. The use of pan-genomes and pan-transcriptomes will improve the efficiency of the study and the total number of predicted lncRNAs compared to using the genome of a single species representative. This review focuses on describing the molecular and biological functions of lncRNAs, experimental and bioinformatic methods of identification, patterns of evolution, detection and analysis of lncRNAs at the scale of pan-genomes and pan-transcriptomes.

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About the authors

А. Y. Pronozin

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences

Author for correspondence.
Email: pronozinartem95@gmail.com

Kurchatov Genomic Center

Russian Federation, Novosibirsk; Novosibirsk

D. A. Afonnikov

Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences; Novosibirsk National Research State University

Email: pronozinartem95@gmail.com

Kurchatov Genomic Center

Russian Federation, Novosibirsk; Novosibirsk; Novosibirsk

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2. 1. Classification of DNRNAS based on location and orientation relative to nearby or overlapping protein-coding genes.

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3. Fig. 2. Molecular functions of dnRNA: a – signaling, DNRNAS receive a signal for interaction with chromatin–modifying enzymes to regulate transcription; b - traps, bind proteins and prevent them from attaching to target genes; c – guides, direct transcription factors to their functioning sites, promote the necessary state of chromatin; d – scaffolds, combine proteins into complexes and initiate various biological processes; d – enhancers, can transcriptionally activate neighboring genes.

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4. 3. Mechanisms of dnRNA–microRNA interaction: a – degradation of dnRNA during microRNA insertion; b – dnRNA acts as a target (sponge) for microRNA; c – dnRNA competes with microRNA to regulate the level of mRNA expression; d – dnRNA acts as a precursor of microRNA (spliced into microRNA).

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5. 4. The biological role of dnRNA in plants. DNRNAS are involved in the regulation of genes responsible for plant resistance to various types of stress (blue rectangle), also affect plant fertility (red rectangle), participate in the development of leaves, roots (green, purple rectangle) and in the processes of vernalization (orange rectangle).

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