Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses

Li, Chunmei; Lai, Xiaofeng; Yu, Xuanyue; Xiong, Zhiwen; Chen, Jie; Lang, Xingxuan; Feng, Haotian; Wan, Xiaorong; Liu, Kai

doi:10.1016/j.bbrc.2023.05.103

Cited by 6 publications

(3 citation statements)

References 77 publications

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“…To further annotate lncRNAs, their secondary structures will need to be explored at a higher resolution. New sources of lncRNAs were continually being identified and classified ( Chorostecki et al., 2023 ; Li C. et al, 2023 ; Mattick et al., 2023 ).…”

Section: Discussion and Prospectsmentioning

confidence: 99%

Update on functional analysis of long non-coding RNAs in common crops

Zhang,

Pi,

Wang

et al. 2024

Front. Plant Sci.

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With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

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Section: Discussion and Prospectsmentioning

confidence: 99%

Update on functional analysis of long non-coding RNAs in common crops

Zhang,

Pi,

Wang

et al. 2024

Front. Plant Sci.

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“…Trimmed Mean of M-values (TMM) was used as the normalization method, and Count Per Million smaller than one (CPM < 1) was used to filter out low-count genes. Given the typically lower expression levels of lncRNAs compared to messenger RNAs (mRNAs) ( Grammatikakis and Lal, 2022 ; Li et al., 2023 ), a threshold of significance was established for lncRNA differential expression, requiring a minimum |log2 fold change| > 0.5. Additionally, lncRNAs with a false discovery rate exceeding 0.05 were excluded.…”

Section: Methodsmentioning

confidence: 99%

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

Babaei,

Bhalla,

Singh

2024

Front. Plant Sci.

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IntroductionWheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development.MethodsThis study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars. Results and discussionWe identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain. ConclusionOur results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.

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“…It has been shown that lncRNAs could act in a cis or trans fashion to control gene expression at transcriptional and post-transcriptional levels, executing as signals, decoys, guides, or scaffolds [ 22 , 23 ], and many studies have shown that lncRNAs can act as “competing endogenous RNA” (ceRNA) by competing with mRNAs to bind to miRNAs and changing the expression of the miRNA target genes [ 24 ]. Some lncRNAs have been suggested to play important regulatory roles in plant defense systems and to be involved in responses to viral, fungal, and bacterial infections in plants [ 14 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 ]. Phytoplasma is an unculturable obligate parasitic pathogen, and despite the fact that several potential virulence factors have been discovered recently, its pathogenic mechanism is still unknown [ 41 , 42 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of lncRNAs and mRNAs Reveals Complex Gene Network Mediated by lncRNAs and Regulatory Function of MuLRR-RLK-AS in Response to Phytoplasma Infection in Mulberry

Liu,

Zhao

et al. 2024

Biomolecules

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Phytoplasma disease is one of the most serious infectious diseases that affects the growth and development of mulberry. Long non-coding RNAs (lncRNAs) play an important role in plants’ defense systems; however, the contribution of lncRNAs in the response to phytoplasma infection in mulberry is still largely unknown. Herein, strand-specific RNA sequencing was performed to profile the mRNAs and lncRNAs involved in the response to phytoplasma infection in mulberry, and a total of 4169 genes were found to be differentially expressed (DE) between healthy and phytoplasma-infected leaves. Moreover, 1794 lncRNAs were identified, of which 742 lncRNAs were DE between healthy and infected leaves. Target prediction showed that there were 68 and 44 DE lncRNAs which may function as cis and trans-regulators, targeting 54 and 44 DE genes, respectively. These DE target genes are associated with biological processes such as metabolism, signaling, development, transcriptional regulation, etc. In addition, it was found that the expression of the antisense lncRNA (MuLRR-RLK-AS) of the leucine-rich repeat receptor-like protein kinase gene (MuLRR-RLK) was decreased in the phytoplasma-infected leaves. Interestingly, it was found that overexpression of MuLRR-RLK-AS can inhibit the expression of MuLRR-RLK. Moreover, it was found that the expression levels of PTI-related and MAPK genes in the transgenic MuLRR-RLK Arabidopsis plants were significantly higher than those in the wild-type plants when inoculated with pathogens, and the transgenic plants were conferred with strong disease resistance. Our results demonstrate that MuLRR-RLK-AS, as a trans-regulatory factor, can inhibit the expression of the MuLRR-RLK gene and is a negative regulatory factor for mulberry resistance. The information provided is particularly useful for understanding the functions and mechanisms of lncRNAs in the response to phytoplasma infection in mulberry.

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Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses

Cited by 6 publications

References 77 publications

Update on functional analysis of long non-coding RNAs in common crops

Update on functional analysis of long non-coding RNAs in common crops

Identifying long non-coding RNAs involved in heat stress response during wheat pollen development

Integrated Analysis of lncRNAs and mRNAs Reveals Complex Gene Network Mediated by lncRNAs and Regulatory Function of MuLRR-RLK-AS in Response to Phytoplasma Infection in Mulberry

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