Genome-wide analysis reveals the crucial role of lncRNAs in regulating the expression of genes controlling pollen development

• Published in: Plant cell reports 2023-02, Vol.42 (2), p.337-354
• Main Authors: Lohani, Neeta, Golicz, Agnieszka A., Allu, Annapurna D., Bhalla, Prem L., Singh, Mohan B.
• Format: Article
• Language: English
• Subjects: Annotations; Biological activity; Biomedical and Life Sciences; Biotechnology; Brassica; Brassica rapa; Brassica rapa - genetics; Cell Biology; Gene expression; Gene Expression Profiling; Genes; Genomes; Genomics; Life Sciences; Males; Mustard; Non-coding RNA; Original Article; Plant Biochemistry; Plant reproductive structures; Plant Sciences; Pollen; Pollen - genetics; Pollen - metabolism; Proteins; Reproduction (biology); Reproductive organs; RNA, Long Noncoding - genetics; Sexual reproduction; Specifications; Transcriptome - genetics; Transcriptomes
• ISSN: 0721-7714; 1432-203X
• DOI: 10.1007/s00299-022-02960-0

Key message The genomic location and stage-specific expression pattern of many long non-coding RNAs reveal their critical role in regulating protein-coding genes crucial in pollen developmental progression and male germ line specification. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 bp with no apparent protein-coding potential. Multiple investigations have revealed high expression of lncRNAs in plant reproductive organs in a cell and tissue-specific manner. However, their potential role as essential regulators of molecular processes involved in sexual reproduction remains largely unexplored. We have used developing field mustard (Brassica rapa) pollen as a model system for investigating the potential role of lncRNAs in reproductive development. Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.