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

Dhiman, Heena; Kapoor, Shruti; Sivadas, Ambily; Sivasubbu, Sridhar; Scaria, Vinod

doi:10.1371/journal.pone.0129997

Cited by 23 publications

(19 citation statements)

References 38 publications

(40 reference statements)

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“…Using the in-house “RNA-seq data analysis pipeline”, we obtained our final dataset with more zebrafish lncRNAs, containing in total 13,604 lncRNA genes (21,128 transcripts) (Additional file 2 ). The major data sources of our lncRNA set are from RNA-seq data analysis and NONCODE [ 22 ], followed by NCBI, Ensembl and zflncRNApedia orderly [ 23 – 25 ] (Fig. 1b ).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Chen

Zhang

et al. 2018

BMC Genomics

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BackgroundZebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs’ function and conservation is really intriguing.ResultsWe systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts.ConclusionsBy integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4458-7) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Chen

Zhang

et al. 2018

BMC Genomics

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“…Transcriptomic studies of early embryonic development 23,25 and five adult tissues 26 have identified over 2,000 lncRNAs in zebrafish 27 , of which 727 have been confirmed as noncoding based on ribosome occupancy patterns 28 . For our knockout study we selected 24 bona fide lncRNAs based on conservation, expression dynamics and proximity to developmental regulatory genes (see Fig 1 for selection criteria for each lncRNA).…”

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confidence: 99%

Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility

Goudarzi

Berg

Pieper

et al. 2018

Preprint

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Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs are dispensable for embryogenesis, viability and fertility.

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“…Regulation of kalrna by lncRNA is not known. Thus, we checked for presence of any lncRNA near the 5′ locus of kalrna in the zebrafish lncRNA database zflncRNApedia (Dhiman et al, 2015). We found one such lncRNA ZF_LNC002146 in the database; although its location is ~72 kb away from kalrna according to Zv9 annotation, overlaps with extended 5′ exon of kalrna in Zv10 (Figure 1A).…”

Section: Resultsmentioning

confidence: 99%

A Novel Long Non-coding RNA, durga Modulates Dendrite Density and Expression of kalirin in Zebrafish

Sarangdhar

Chaubey

Bhatt

et al. 2017

Front. Mol. Neurosci.

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Kalirin, a key player in axonal development, nerve growth and synaptic re-modeling, is implicated in many pathological conditions like schizophrenia and autism-spectrum disorders. Alternative promoters and splicing lead to functionally distinct isoforms, but the post-transcriptional regulation of Kalirin has not been studied. Here, we report a novel non-coding RNA, which we name durga, arising from the first exon of kalirin a (kalrna) in the antisense orientation in zebrafish. The kalrna and durga transcripts are barely detectable during early development, but steadily increase by 24 hours post-fertilization (hpf) as the brain develops. Over-expression of durga in the zebrafish embryo led to an increase in kalrna expression. The morphology of the neurons cultured from durga injected embryos had significantly fewer and shorter dendrites. Although durga has no apparent sequence homolog in mammals, based on gene synteny, we found a non-coding RNA arising from the 5′ end of the human Kalrn gene and expressed in the human neuronal cell line, SH-SY5Y. We propose that the zebrafish lncRNA durga maintains dendritic length and density through regulation of kalrna expression and this may have further implications in mammalian systems.

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

Cited by 23 publications

References 38 publications

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility

A Novel Long Non-coding RNA, durga Modulates Dendrite Density and Expression of kalirin in Zebrafish

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