PLNlncRbase: A resource for experimentally identified lncRNAs in plants

Xuan, Hongdong; Zhang, Linzhong; Liu, Xueshi; Han, Guomin; Li, Juan; Li, Xin; Liu, Aiguo; Liao, Mingzhi; Zhang, Shihua

doi:10.1016/j.gene.2015.07.069

Cited by 66 publications

(39 citation statements)

References 48 publications

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“…The noncoding high‐quality reads were fed into C‐mii tool (http://www.biotec.or.th/isl/c-mii) for identification of miRNAs. This tool does homology search against the miRBase database, comprised of known plant miRNAs, and evaluates the stability of secondary structures of the predicted precursor miRNAs . The rose‐scented geranium miRNAs were predicted on the default criteria of 18–32 nucleotides length, less than three mismatches, relatively high AU content than GC, and highly negative minimal folding free energy (MFE) and MFE index (MFEI) value.…”

Section: Methodsmentioning

confidence: 99%

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

2019

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This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose‐scented geranium. We analyzed RNA‐seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose‐scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real‐time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose‐scented geranium.

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Section: Methodsmentioning

confidence: 99%

Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose‐scented geranium

2019

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“…The transcriptional control activity of lncRNAs in stress conditions has already been reported in Arabidopsis for the TFs auxin‐regulated promoter loop RNA (APOLO) and At4/induced by Pi starvation I (IPSI), involved in root development and phosphate homeostasis, respectively (Sun et al ., ; Csorba et al ., ; reviewed by Bazin and Bailey‐Serres, ). Well established plant database and online prediction tools like PLNlncbase and GREENC, offer a list of lncRNAs and their functions when known, (Xuan et al ., ; this article also lists public repositories; Paytuví Gallart et al ., ). As of today, there is yet no approach based on lncRNAs applied to the study of signalling pathways in planta .…”

Section: Synthetic Molecular Toolboxmentioning

confidence: 99%

Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms

Braguy

Zurbriggen

2016

The Plant Journal

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SUMMARYPlants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.

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“…With the recent developments in bioinformatics and sequencing, in particular transcriptomics (RNA sequencing), knowledge on non-coding RNAs (ncRNA) is expanding quickly , including the development of databases for ncRNAs (Xuan et al 2015, Patra et al 2014. This may become a driver of RNAi-based methods, as there is still much unknown about mechanisms of RNA-based signalling pathways and control of development in plants, in which also histone modifications play a role (Matzke & Mosher 2014).…”

Section: Application Areasmentioning

confidence: 99%