Abstract
BACKGROUND: Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to noncoding RNAs (ncRNAs). Moreover, increasing evidence indicates that an intricate interplay among RNA species, including protein-coding RNAs and ncRNAs, exists in eukaryotic transcriptomes, however, it remains elusive in plant leaves. RESULTS: We detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves. Transcriptome profiling showed extensive changes during leaf development. In addition, comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves. To investigate the complex post-transcriptional interactions in Arabidopsis leaves, we constructed a global circRNA/lncRNA-associated ceRNA network. Functional analysis revealed that ceRNAs were highly correlated with leaf development. These ceRNAs could be divided into six clusters, which were enriched for different functional classes. Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs. CONCLUSIONS: Our results demonstrate that understanding the ceRNA interactions will lead insights into gene regulations implicated in leaf development.
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Claims 6
Claim · model-written summary
Novel circular and long noncoding RNAs were detected in Arabidopsis leaves.
- Taxon
- Arabidopsis
Arabidopsise0 - Organ / stage
- leavese0
- Outcome
- novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs)e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves.”
Claim · model-written summary
Arabidopsis leaf transcriptomes changed extensively during development.
- Taxon
- ArabidopsisArabidopsist0
- Organ / stage
- leaft0
- Outcome
- Transcriptome profilinge0
- Direction
- extensive changese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Transcriptome profiling showed extensive changes during leaf development.”
t0“Arabidopsis leaf development”
Claim · model-written summary
Circular RNAs were widespread in leaves of other plants.
Verbatim
e0“comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves.”
Claim · model-written summary
Competitive endogenous RNAs were highly correlated with Arabidopsis leaf development.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- ceRNAse0
- Outcome
- leaf developmente0
- Direction
- highly correlatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Functional analysis revealed that ceRNAs were highly correlated with leaf development.”
t0“Arabidopsis leaf development”
Claim · model-written summary
The competitive endogenous RNAs formed six clusters enriched for different functional classes.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- ceRNAse0
- Outcome
- six clusterse0
- Qualifier
- enriched for different functional classese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These ceRNAs could be divided into six clusters, which were enriched for different functional classes.”
t0“Arabidopsis”
Claim · model-written summary
Stage common and stage specific hub competitive endogenous RNAs had different roles in Arabidopsis leaf development.
- Taxon
- ArabidopsisArabidopsist0
- Organ / stage
- leaft0
- Gene
- stage common and specific hub ceRNAse0
- Outcome
- different rolese0
- Direction
- differente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs.”
t0“Arabidopsis leaf development”