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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.


Related in: MedlinePlus

Features of lncRNA1840 and 1459. Analysis of expression of lncRNA1840 (A) and lncRNA1459 (B) during fruit ripening. Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that at the IM stage of AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. IM, immature green; MG, mature green; BR, breaker; PK, pink; RR, red-ripe stage. (C) Determination of the 3′ end structure of lncRNAs. Random-primed RT–PCR was performed on total RNAs, poly(A)+, and poly(A)– RNAs from tomato fruits to detect novel lncRNAs. (D) Analysis of the 5′ end structure of lncRNAs. Total RNAs from tomato fruits were treated (+) or not (–) with various enzymes and subjected to random-primed RT–PCR to detect specific lncRNAs. RppH, 5′ pyrophosphohydrolase; XRN-1, 5′ to 3′ exoribonuclease; PNK, polynucleotide kinase. –RT, reverse transcription was performed in the absence of reverse transcriptase. Transcript from RIN was detected by RT–PCR as a control for poly(A)+ RNA and capped RNA. PCRs with genomic DNA were used as positive controls. The amplification region of RIN primers contained one intron which results in a larger PCR product of DNA template than the others.
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Figure 8: Features of lncRNA1840 and 1459. Analysis of expression of lncRNA1840 (A) and lncRNA1459 (B) during fruit ripening. Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that at the IM stage of AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. IM, immature green; MG, mature green; BR, breaker; PK, pink; RR, red-ripe stage. (C) Determination of the 3′ end structure of lncRNAs. Random-primed RT–PCR was performed on total RNAs, poly(A)+, and poly(A)– RNAs from tomato fruits to detect novel lncRNAs. (D) Analysis of the 5′ end structure of lncRNAs. Total RNAs from tomato fruits were treated (+) or not (–) with various enzymes and subjected to random-primed RT–PCR to detect specific lncRNAs. RppH, 5′ pyrophosphohydrolase; XRN-1, 5′ to 3′ exoribonuclease; PNK, polynucleotide kinase. –RT, reverse transcription was performed in the absence of reverse transcriptase. Transcript from RIN was detected by RT–PCR as a control for poly(A)+ RNA and capped RNA. PCRs with genomic DNA were used as positive controls. The amplification region of RIN primers contained one intron which results in a larger PCR product of DNA template than the others.

Mentions: For further characterization of lncRNA1840 and lncRNA1459, the expression pattern of thse lncRNAs during fruit ripening was first explored. The transcripts of lncRNA1840 accumulated to a high level at the IM stage, and then the expression levels dropped to the lowest at the MG stage. As the fruit became red, lncRNA1840 increased rapidly up to the RR stage (Fig. 8A). However, expression of lncRNA1459 increased during fruit ripening, peaking at the PK stage (Fig. 8B). The transcriptional patterns of both lncRNA1840 and lncRNA1459 indicated that they were ripening related.


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)

Features of lncRNA1840 and 1459. Analysis of expression of lncRNA1840 (A) and lncRNA1459 (B) during fruit ripening. Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that at the IM stage of AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. IM, immature green; MG, mature green; BR, breaker; PK, pink; RR, red-ripe stage. (C) Determination of the 3′ end structure of lncRNAs. Random-primed RT–PCR was performed on total RNAs, poly(A)+, and poly(A)– RNAs from tomato fruits to detect novel lncRNAs. (D) Analysis of the 5′ end structure of lncRNAs. Total RNAs from tomato fruits were treated (+) or not (–) with various enzymes and subjected to random-primed RT–PCR to detect specific lncRNAs. RppH, 5′ pyrophosphohydrolase; XRN-1, 5′ to 3′ exoribonuclease; PNK, polynucleotide kinase. –RT, reverse transcription was performed in the absence of reverse transcriptase. Transcript from RIN was detected by RT–PCR as a control for poly(A)+ RNA and capped RNA. PCRs with genomic DNA were used as positive controls. The amplification region of RIN primers contained one intron which results in a larger PCR product of DNA template than the others.
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Related In: Results  -  Collection

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Figure 8: Features of lncRNA1840 and 1459. Analysis of expression of lncRNA1840 (A) and lncRNA1459 (B) during fruit ripening. Actin expression values were used for internal reference. The relative level of lncRNA transcripts was normalized to that at the IM stage of AC fruits where the amount was arbitrarily assigned a value of 1. Error bars indicate ±SD of three biological replicates, each measured in triplicate. IM, immature green; MG, mature green; BR, breaker; PK, pink; RR, red-ripe stage. (C) Determination of the 3′ end structure of lncRNAs. Random-primed RT–PCR was performed on total RNAs, poly(A)+, and poly(A)– RNAs from tomato fruits to detect novel lncRNAs. (D) Analysis of the 5′ end structure of lncRNAs. Total RNAs from tomato fruits were treated (+) or not (–) with various enzymes and subjected to random-primed RT–PCR to detect specific lncRNAs. RppH, 5′ pyrophosphohydrolase; XRN-1, 5′ to 3′ exoribonuclease; PNK, polynucleotide kinase. –RT, reverse transcription was performed in the absence of reverse transcriptase. Transcript from RIN was detected by RT–PCR as a control for poly(A)+ RNA and capped RNA. PCRs with genomic DNA were used as positive controls. The amplification region of RIN primers contained one intron which results in a larger PCR product of DNA template than the others.
Mentions: For further characterization of lncRNA1840 and lncRNA1459, the expression pattern of thse lncRNAs during fruit ripening was first explored. The transcripts of lncRNA1840 accumulated to a high level at the IM stage, and then the expression levels dropped to the lowest at the MG stage. As the fruit became red, lncRNA1840 increased rapidly up to the RR stage (Fig. 8A). However, expression of lncRNA1459 increased during fruit ripening, peaking at the PK stage (Fig. 8B). The transcriptional patterns of both lncRNA1840 and lncRNA1459 indicated that they were ripening related.

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.


Related in: MedlinePlus