A Walkthrough to the Use of GreeNC: The Plant lncRNA Database

Paytuví-Gallart, Andreu; Sanseverino, Walter; Cigliano, Riccardo Aiese

doi:10.1007/978-1-4939-9045-0_25

Cited by 7 publications

(6 citation statements)

References 68 publications

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“…However, interestingly, nearly 11% showed synteny with Vitis vinifera, which is very distantly related to chickpea, thus suggesting that some lncRNAs are evolutionarily conserved. This finding may aid in comparative studies to functionally annotate lncRNAs (Paytuvi-Gallart et al, 2019). According to lncRNAdb (http://www.…”

Section: Functional Annotation Of Lncrnas Through Orthologous Inferencementioning

confidence: 98%

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea

Kaashyap

Kaur

Ford

et al. 2022

Plant Biotechnology Journal

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Salinity severely affects the yield of chickpea. Understanding the role of lncRNAs can shed light on chickpea salt tolerance mechanisms. However, because lncRNAs are encoded by multiple sites within the genome, their classification to reveal functional versatility at the transcriptional and the post-transcriptional levels is challenging. To address this, we deep sequenced 24 saltchallenged flower transcriptomes from two parental genotypes of a RIL population that significantly differ in salt tolerance ability. The transcriptomes for the first time included 12 polyadenylated and 12 non-polyadenylated RNA libraries to a sequencing depth of ~50 million reads. The ab initio transcriptome assembly comprised ~34 082 transcripts from three biological replicates of salt-tolerant (JG11) and salt-sensitive (ICCV2) flowers. A total of 9419 lncRNAs responding to salt stress were identified, 2345 of which were novel lncRNAs specific to chickpea. The expression of poly(A+) lncRNAs and naturally antisense transcribed RNAs suggest their role in post-transcriptional modification and gene silencing. Notably, 178 differentially expressed lncRNAs were induced in the tolerant genotype but repressed in the sensitive genotype. Coexpression network analysis revealed that the induced lncRNAs interacted with the FLOWERING LOCUS (FLC), chromatin remodelling and DNA methylation genes, thus inducing flowering during salt stress. Furthermore, 26 lncRNAs showed homology with reported lncRNAs such as COOLAIR, IPS1 and AT4, thus confirming the role of chickpea lncRNAs in controlling flowering time as a crucial salt tolerance mechanism in tolerant chickpea genotype. These robust set of differentially expressed lncRNAs provide a deeper insight into the regulatory mechanisms controlled by lncRNAs under salt stress.

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Section: Functional Annotation Of Lncrnas Through Orthologous Inferencementioning

confidence: 98%

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea

Kaashyap

Kaur

Ford

et al. 2022

Plant Biotechnology Journal

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“…Numerous other databases of lncRNAs are available; however, most of these are subsets of the databases covered here (NONCODE, FANTOM CAT, etc. ), or were constructed for a specific purpose, such as for a particular disease (Lnc2Cancer [ 16 ]) or species (GreeNC [ 17 ]).…”

Section: General Lncrna Databasesmentioning

confidence: 99%

“…Although no comprehensive review of lncRNA databases has been published recently, there are a multitude of different databases available, ranging from general to highly specific. These include but are not limited to: MONOCLdb for mouse lung lncRNAs [ 35 ], the Cancer lncRNA Census [ 36 ] and GreenNC for plant lncRNAs [ 17 ]. LncRNAs often have several different identifiers, including gene IDs, HUGO gene names, ENSEMBL identifiers, ENTREZ gene IDs and many more.…”

Section: General Lncrna Databasesmentioning

confidence: 99%

The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis

Pinkney

Wright

Diermeier

2020

ncRNA

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Long non-coding RNAs (lncRNAs) are a rapidly expanding field of research, with many new transcripts identified each year. However, only a small subset of lncRNAs has been characterized functionally thus far. To aid investigating the mechanisms of action by which new lncRNAs act, bioinformatic tools and databases are invaluable. Here, we review a selection of computational tools and databases for the in silico analysis of lncRNAs, including tissue-specific expression, protein coding potential, subcellular localization, structural conformation, and interaction partners. The assembled lncRNA toolkit is aimed primarily at experimental researchers as a useful starting point to guide wet-lab experiments, mainly containing multi-functional, user-friendly interfaces. With more and more new lncRNA analysis tools available, it will be essential to provide continuous updates and maintain the availability of key software in the future.

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“…Among them, long ncRNAs (lncRNAs; longer that 200 bases and showing poor coding capacity) can act directly as long transcripts or can be processed into a rich diversity of functional small RNAs. In plants, thousands of lncRNAs have been annotated in at least 40 species [10,11]. According to their genomic position in relation to protein-coding genes, lncRNAs can be classified as antisense, intronic, intergenic, or promoter transcripts [3].…”

Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs shape transcription in plants

et al. 2020

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The advent of novel high-throughput sequencing techniques has revealed that eukaryotic genomes are massively transcribed although only a small fraction of RNAs exhibits protein-coding capacity. In the last years, long noncoding RNAs (lncRNAs) have emerged as regulators of eukaryotic gene expression in a wide range of molecular mechanisms. Plant lncRNAs can be transcribed by alternative RNA polymerases, acting directly as long transcripts or can be processed into active small RNAs. Several lncRNAs have been recently shown to interact with chromatin, DNA or nuclear proteins to condition the epigenetic environment of target genes or modulate the activity of transcriptional complexes. In this review, we will summarize the recent discoveries about the actions of plant lncRNAs in the regulation of gene expression at the transcriptional level.

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A Walkthrough to the Use of GreeNC: The Plant lncRNA Database

Cited by 7 publications

References 68 publications

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea

Comprehensive transcriptomic analysis of two RIL parents with contrasting salt responsiveness identifies polyadenylated and non‐polyadenylated flower lncRNAs in chickpea

The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis

Long noncoding RNAs shape transcription in plants

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