Absence of CG methylation alters the long noncoding transcriptome landscape in multiple species

Zhao, Ting; Mei, Huan; Cao, Zijian; Wang, Luyao; Tao, Xiaochun; Feng, Shouli; Fang, Lei; Guan, Xueying

doi:10.1002/1873-3468.14100

Cited by 4 publications

(4 citation statements)

References 68 publications

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“…Similar research results indicate that lincRNAs also has methylation process, which is different from mRNAs lincRNAs had different DNA methylation profiles (Wang M. H. et al, 2018). And the researchers found that lincRNAs were obviously activated after CG DNA methylation (Zhao et al, 2021). Other studies have shown that the lincRNAs have two regulation of gene expression, cis and trans manner (Zhang et al, 2014;Quan et al, 2015).…”

Section: Discussionmentioning

confidence: 71%

“…Later research found that long non-coding RNAs with potential functions in gene regulation are widespread throughout the transcriptome (Iyer et al, 2015). The non-coding region of the genome is largely composed of transposable elements, some of which are functionalized with lincRNAs (Zhao et al, 2021). How lincRNA regulates the expression of susceptibility or resistance genes in tomato to play what role needs further study.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato (Solanum lycopersicum)

et al. 2022

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There is growing evidences indicating that long intergenic ncRNAs (lincRNAs) play key roles in plant development and stress responses. To research tomato lincRNA functions during the interaction between tomato and Ralstonia solanacearum, RNA-seq data of tomato plants inoculated with R. solanacearum was analyzed. In this study, 315 possible lincRNAs were identified from RNA-seq data. Then 23 differentially expressed lincRNAs between tomato plants inoculated with R. solanacearum and control were identified and a total of 171 possible target genes for these differentially expressed lincRNAs were predicted. Through GO and KEGG analysis, we found that lincRNA might be involved in jasmonic acid and ethylene signaling pathways to respond to tomato bacterial wilt infection. Furthermore, lincRNA may also be involved in regulating the expression of AGO protein. Subsequently, analysis of expression patterns between differentially expressed lincRNAs and adjacent mRNAs by qRT-PCR revealed that part of lincRNAs and their possible target genes exhibited positive correlation. Taken together, these results suggest that lincRNAs play potential roles in tomato against R. solanacearum infection and will provide fundamental information about the lincRNA-based plant defense mechanisms.

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Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato (Solanum lycopersicum)

et al. 2022

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“…1 B, lower part). In addition, absence of mCG in DNA methylation mutants has more impact on lincRNA transcription, compared to non-CG methylation in A. thaliana , O. sativa , and S. lycopersicum [60] . Hence, epigenetic modifiers universally determine transcription of protein coding genes, but their possibilities to affect transcription of lncRNA regions seem to be concerned.…”

Section: Survey Of Functional Lncrnas Associated With Epigenetic Modi...mentioning

confidence: 94%

Epigenetic modifications: Allusive clues of lncRNA functions in plants

Yang¹,

Bai²,

Li³

et al. 2023

Computational and Structural Biotechnology Journal

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“…The connection between lncRNAs and transposable elements, and between lncRNAs and DNA CG methylation [52,53] 4…”

Section: Introductionmentioning

confidence: 99%

Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing

et al. 2021

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As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.

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Absence of CG methylation alters the long noncoding transcriptome landscape in multiple species

Cited by 4 publications

References 68 publications

Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato (Solanum lycopersicum)

Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato (Solanum lycopersicum)

Epigenetic modifications: Allusive clues of lncRNA functions in plants

Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing

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