Abstract
Leaf senescence, the last stage of leaf development, is essential for whole-plant fitness as it marks the relocation of nutrients from senescing leaves to reproductive or other developing organs. Temporally coordinated physiological and functional changes along leaf aging are fine-tuned by a highly regulated genetic program involving multi-layered regulatory mechanisms. Long noncoding RNAs (lncRNAs) are newly emerging as hidden players in many biological processes; however, their contribution to leaf senescence has been largely unknown. Here, we performed comprehensive analyses of RNA-seq data representing all developmental stages of leaves to determine the genome-wide lncRNA landscape along leaf aging. A total of 771 lncRNAs, including 232 unannotated lncRNAs, were identified. Time-course analysis revealed 446 among 771 developmental age-related lncRNAs (AR-lncRNAs). Intriguingly, the expression of AR-lncRNAs was regulated more dynamically in senescing leaves than in growing leaves, revealing the relevant contribution of these lncRNAs to leaf senescence. Further analyses enabled us to infer the function of lncRNAs, based on their interacting miRNA or mRNA partners. We considered functionally diverse lncRNAs including antisense lncRNAs (which regulate overlapping protein-coding genes), competitive endogenous RNAs (ceRNAs; which regulate paired mRNAs using miRNAs as anchors), and mRNA-interacting lncRNAs (which affect the stability of mRNAs). Furthermore, we experimentally validated the senescence regulatory function of three novel AR-lncRNAs including one antisense lncRNA and two mRNA-interacting lncRNAs through molecular and phenotypic analyses. Our study provides a valuable resource of AR-lncRNAs and potential regulatory networks that link the function of coding mRNA and AR-lncRNAs. Together, our results reveal AR-lncRNAs as important elements in the leaf senescence process.
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Claims 6
Claim · model-written summary
The analysis identified 771 lncRNAs, including 232 unannotated lncRNAs.
- Taxon
- Arabidopsis
Arabidopsist0 - Outcome
- lncRNAse0
- Value
- 771e0
Not reportedOrgan / stage
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total of 771 lncRNAs, including 232 unannotated lncRNAs, were identified.”
t0“Arabidopsis”
Claim · model-written summary
Among identified lncRNAs, 232 were unannotated.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- unannotated lncRNAse0
- Value
- 232e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total of 771 lncRNAs, including 232 unannotated lncRNAs, were identified.”
t0“Arabidopsis”
Claim · model-written summary
Time-course analysis identified 446 developmental age-related lncRNAs among 771 lncRNAs.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- developmental age-related lncRNAs (AR-lncRNAs)e0
- Value
- 446e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Time-course analysis revealed 446 among 771 developmental age-related lncRNAs (AR-lncRNAs).”
t0“Arabidopsis”
Claim · model-written summary
AR-lncRNA expression changed more dynamically in senescing than growing leaves.
- Taxon
- ArabidopsisArabidopsist0
- Organ / stage
- senescing leavese0
- Gene
- AR-lncRNAse0
- Outcome
- expression of AR-lncRNAse0
- Direction
- more dynamicallye0
- Comparator
- growing leavese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the expression of AR-lncRNAs was regulated more dynamically in senescing leaves than in growing leaves”
t0“Arabidopsis”
Claim · model-written summary
Analyses inferred lncRNA functions from interacting miRNA or mRNA partners.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- function of lncRNAse0
- Comparator
- interacting miRNA or mRNA partnerse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Further analyses enabled us to infer the function of lncRNAs, based on their interacting miRNA or mRNA partners.”
t0“Arabidopsis”
Claim · model-written summary
Molecular and phenotypic analysis validated senescence regulatory functions for three novel AR-lncRNAs.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- AR-lncRNAse0
- Outcome
- senescence regulatory functione0
- Value
- threee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we experimentally validated the senescence regulatory function of three novel AR-lncRNAs including one antisense lncRNA and two mRNA-interacting lncRNAs through molecular and phenotypic analyses.”
t0“Arabidopsis”