PLncDB: plant long non-coding RNA database

Jin, Jingjing; Li, Jun; Wang, Huan; Wong, Limsoon; Chua, Nam‐Hai

doi:10.1093/bioinformatics/btt107

Cited by 164 publications

(118 citation statements)

References 39 publications

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“…Moreover, an updated version of the Noncode database is now available as Noncode v4.0 (Xie et al 2014). Also we note that, apart from the resources reviewed here, other specific tools and databases exist, such as PLncDB (plant related lncRNAs) (Jin et al 2013), NRED (noncoding expression database) (Dinger et al 2009), and Linc2go ).…”

Section: Discussionmentioning

confidence: 99%

Databases for lncRNAs: a comparative evaluation of emerging tools

Fritah

Niclou

Azuaje

2014

RNA

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The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.

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Section: Discussionmentioning

confidence: 99%

Databases for lncRNAs: a comparative evaluation of emerging tools

Fritah

Niclou

Azuaje

2014

RNA

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“…We used plant long noncoding RNA database (PLncDB) to browse the high through-put datasets (Jin et al, 2013). RNA-seq or ChIP-seq sequences were aligned to the TAIR10 genome using TopHat, SAMtools, BEDTools, and a custom PERL script (Li et al, 2009;Quinlan and Hall, 2010).…”

Section: Analysis Of Rna-seq Datasetsmentioning

confidence: 99%

“…BigWig-formatted files were integrated into PLncDB. Construction methods of PLncDB were described in our previous study (Jin et al, 2013).…”

Section: Analysis Of Rna-seq Datasetsmentioning

confidence: 99%

CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis

et al. 2016

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ORCID IDs: 0000-0003-1338-523X (J.L.); 0000-0001-6872-9373 (S.D.).CURLY LEAF (CLF), a histone methyltransferase of Polycomb Repressive Complex 2 (PRC2) for trimethylation of histone H3 Lys 27 (H3K27me3), has been thought as a negative regulator controlling mainly postgermination growth in Arabidopsis (Arabidopsis thaliana). Approximately 14% to 29% of genic regions are decorated by H3K27me3 in the Arabidopsis genome; however, transcriptional repression activities of PRC2 on a majority of these regions remain unclear. Here, by analysis of transcriptome profiles, we found that approximately 11.6% genes in the Arabidopsis genome were repressed by CLF in various organs. Unexpectedly, approximately 54% of these genes were preferentially repressed in siliques. Further analyses of 118 transcriptome datasets uncovered a group of genes that was preferentially expressed and repressed by CLF in embryos at the mature-green stage. This observation suggests that CLF mediates a large-scale H3K27me3 programming/reprogramming event during embryonic development. Plants of clf-28 produced bigger and heavier seeds with higher oil content, larger oil bodies, and altered long-chain fatty acid composition compared with wild type. Around 46% of CLF-repressed genes were associated with H3K27me3 marks; moreover, we verified histone modification and transcriptional repression by CLF on regulatory genes. Our results suggest that CLF silences specific gene expression modules. Genes operating within a module have various molecular functions, but they cooperate to regulate a similar physiological function during embryo development.

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“…[8][9][10] A recent study reported 6,480 long intergenic non-coding RNAs (lincRNAs) in Arabidopsis, 11 which have been made available in PLncDB (the plant long non-coding RNA database). 12 On the other hand, the functional significance of the RNA molecules has been suggested to be embedded in the well-organized structures. 13 Thus, one question was raised whether these lncRNAs could form internal structures for certain biological outputs, such as sRNA production just like pri-miRNAs.…”

Section: Introductionmentioning

confidence: 99%