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RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening.

Zhu B, Yang Y, Li R, Fu D, Wen L, Luo Y, Zhu H - J. Exp. Bot. (2015)

Bottom Line: It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening.In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit.Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

No MeSH data available.


Predicted miRNA targets and endogenous target mimcs from lncRNAs. (A) Three lncRNAs as miRNA targets. (B) Three lncRNAs as endogenous target mimics of miRNAs. The blue sequences are tomato miRNAs. The red sequences indicate the regions which were complemented with miRNAs.
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Figure 4: Predicted miRNA targets and endogenous target mimcs from lncRNAs. (A) Three lncRNAs as miRNA targets. (B) Three lncRNAs as endogenous target mimics of miRNAs. The blue sequences are tomato miRNAs. The red sequences indicate the regions which were complemented with miRNAs.

Mentions: Interplay between miRNAs and lncRNAs is one of the important functional patterns seen for lncRNAs (Yoon et al., 2014). LncRNAs could be targeted by miRNAs (Shuai et al., 2014) and could also function as eTMs of miRNAs (Wu et al., 2013). To examine whether lncRNAs are bona fide targets for miRNAs, all of the 3679 lncRNAs we checked using psRNATarget and psRobot. Only three miRNA targets were identified (Fig. 4A). The recovery of a small number of miRNA targets probably resulted from the low expression level of lncRNAs that were not detected by RNA-Seq. Of these three miRNA targets, lncRNA504 was the target of sly-miR6024 that was involved in plant immunity (F. Li et al., 2012). LncRNA3613 was the target of sly-miR5304 that has been only identified in solanaceous plants (Gu et al., 2014). In addition, lncRNA3294 was the target of sly-miR169 that is engaged in drought tolerance of tomato (Zhang et al., 2011).


RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening.

Zhu B, Yang Y, Li R, Fu D, Wen L, Luo Y, Zhu H - J. Exp. Bot. (2015)

Predicted miRNA targets and endogenous target mimcs from lncRNAs. (A) Three lncRNAs as miRNA targets. (B) Three lncRNAs as endogenous target mimics of miRNAs. The blue sequences are tomato miRNAs. The red sequences indicate the regions which were complemented with miRNAs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4507755&req=5

Figure 4: Predicted miRNA targets and endogenous target mimcs from lncRNAs. (A) Three lncRNAs as miRNA targets. (B) Three lncRNAs as endogenous target mimics of miRNAs. The blue sequences are tomato miRNAs. The red sequences indicate the regions which were complemented with miRNAs.
Mentions: Interplay between miRNAs and lncRNAs is one of the important functional patterns seen for lncRNAs (Yoon et al., 2014). LncRNAs could be targeted by miRNAs (Shuai et al., 2014) and could also function as eTMs of miRNAs (Wu et al., 2013). To examine whether lncRNAs are bona fide targets for miRNAs, all of the 3679 lncRNAs we checked using psRNATarget and psRobot. Only three miRNA targets were identified (Fig. 4A). The recovery of a small number of miRNA targets probably resulted from the low expression level of lncRNAs that were not detected by RNA-Seq. Of these three miRNA targets, lncRNA504 was the target of sly-miR6024 that was involved in plant immunity (F. Li et al., 2012). LncRNA3613 was the target of sly-miR5304 that has been only identified in solanaceous plants (Gu et al., 2014). In addition, lncRNA3294 was the target of sly-miR169 that is engaged in drought tolerance of tomato (Zhang et al., 2011).

Bottom Line: It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening.In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit.Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

View Article: PubMed Central - PubMed

Affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

No MeSH data available.