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

Epigenetic modifications: Allusive clues of lncRNA functions in plants

Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized. Moreover, the relationship between lncRNAs and other epigenetic modifications has not been systematically studied. In this mini-review, we briefly summarize the representative biological functions of lncRNAs in developmental programs and environmental responses in plants. In addition, we particularly discuss the intimate relationship between lncRNAs and other epigenetic modifications, and we outline the underlying avenues and challenges for future research on plant lncRNAs.

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

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.

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

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.

The lincRNA XH123 is involved in cotton cold-stress regulation

We characterize a functional lincRNA, XH123 in cotton seedling in defense of cold stress. The silencing of XH123 leads to increased sensitivity to cold stress and the decay of chloroplast. Cotton, which originated from the arid mid-American region, is one of the most important cash crops worldwide. Cultivated cotton is now widely spread throughout high-altitude regions such as those in the far northwest of Asia. In such areas, spring temperatures below 12 ℃ impose cold stress on cotton seedlings, with concomitant threat of lost yield and productivity. It is documented that cold stress can induce differential expression of long noncoding RNAs (lncRNAs) in cotton; however, it is not yet clear if these cold-responsive lncRNAs are actively involved with tolerance of cold stress at the molecular level. Here, we select ten long intergenic non-coding RNAs as candidate genes and use virus-induced gene silencing and additional cold treatments to examine their roles in the response to cold stress during the cotton seedling stage. One such gene, XH123, was revealed to be involved in tolerance of cold stress. Specifically, XH123-silenced plants demonstrated sensitivity to cold stress, exhibiting chloroplast damage and increased endogenous levels of reactive oxygen species. The transcriptome profile of XH123-silenced seedlings was similar to that of cold-stressed seedlings having the known cold stress gene PIF3 silenced. These results imply that the lincRNA XH123 is actively involved with cold stress regulation in cotton during the seedling stage.