zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs

<div><p>Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncRNAs. In the present report, we created a catalog of lncRNAs in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncRNA transcripts in zebrafish. The lncRNAs were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. Analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincRNAs. We created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. The resource also hosts a genome browser where the datasets could be browsed in the genome context. To the best of our knowledge, this is the first comprehensive resource providing a unified catalog of lncRNAs in zebrafish. The resource is freely available at URL: <a href="http://genome.igib.res.in/zflncRNApedia" target="_blank">http://genome.igib.res.in/zflncRNApedia</a></p></div

Workflow detailing data curation and methodologies involved in building the resource.

<p>Workflow detailing data curation and methodologies involved in building the resource.</p

Matrix reporting sample count of various datasets used across different developmental time-points.

<p>Matrix reporting sample count of various datasets used across different developmental time-points.</p

Depicting lncRNA transcripts targeted by miRNAs.

<p>The figure shows the lncRNA transcripts targeted by miRNAs along with the distribution of Ago types in the targeting complex. The presence and absence of specific Ago type in the RISC complex is represented by the difference in the colors in the heatmap. The targeting miRNA has also been mentioned.</p

Contribution of each Ago class in targeting lncRNA.

<p>Contribution of each Ago class in targeting lncRNA.</p

A: Complete interaction network of lncRNA, miRNA and mRNA.

<p>The interaction network wherein the experimental miRNA-mRNA interactions are represented in red nodes, the predicted miRNA-lncRNA interactions are represented in blue nodes and total miRNA-mRNA interactions represented as black nodes. <b>B1:</b> An interesting example from the network highlighted in orange showing interactions between of network highlighting <b>miRNA:</b> (a) hsa-mir-9; <b>lncRNA:</b> (d) ENST00000500197.2, (e) ENST00000509783.1, (f) ENST00000511014.1, (h) ENST00000505030.1, (i) ENST00000504246.1; <b>mRNA:</b> (b) ENST00000384838.1, (c) ENST00000262095.2, (g) ENST00000491143.1, (j) ENST00000226574 <b>B2:</b> Another interesting example from the network highlighted in blue showing interactions between <b>miRNA</b>: (1) hsa-miR-196a, (5) hsa-miR-196b*, (13)hsa- miR-196b; <b>lncRNA</b>: (4) ENST00000523790.1; (6) ENST00000489695.1, (12) ENST00000519935.1; <b>mRNA</b>: (2) ENST00000354032.4, (3) ENST00000384852.1, (7) ENST00000313173, (8) ENST0000024215, (9) ENST00000040584, (10) ENST00000304786.7, (11) ENST00000366839.4.</p

Binding alignments of microRNAs targeting predicted zebrafish lncRNA.

<p>The figure shows predicted binding alignment of miR-125a, miR-125b, miR-125c, miR-17a*, miR-20*, miR-210*, miR-29a, miR-29b and miR457a with predicted zebrafish lncRNA.</p

The number of reads mapping in each of the individual datasets.

<p>The number of reads mapping in each of the individual datasets.</p

Workflow for the analysis of potential microRNA binding sites on lncRNAs and re-construction of the regulatory interactome.

<p>Workflow for the analysis of potential microRNA binding sites on lncRNAs and re-construction of the regulatory interactome.</p

Differentially expressed long non-coding RNAs in 45,X and 46,XX fibroblast cells at P value<0.001 and FDR (q) value<0.05.

<p>Differentially expressed long non-coding RNAs in 45,X and 46,XX fibroblast cells at P value<0.001 and FDR (q) value<0.05.</p