Short Stories on Zebrafish Long Noncoding RNAs

Haque, Syed Ehtaishamul; Kaushik, Kriti; Leonard, Vincent Elvin; Kapoor, Shruti; Sivadas, Ambily; Joshi, Adita; Scaria, Vinod; Sivasubbu, Sridhar

doi:10.1089/zeb.2014.0994

Cited by 24 publications

(18 citation statements)

References 87 publications

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“…Protocols for acute toxicity tests with zebrafish embryos have been worked out [ 7 , 12 ], and good correlations were found between results obtained with zebrafish embryo and acute adult fish toxicity tests for more than 140 chemicals [ 2 , 3 , 13 ]. Furthermore, the availability of detailed information regarding genomics, transcriptomics and metabolomics [ 14 – 17 ] makes zebrafish embryos suitable as model system in molecular ecotoxicology studies [ 10 ]. Zebrafish embryos have been used in some studies on lipid metabolism performed in the context of disease research [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Body Mass Parameters, Lipid Profiles and Protein Contents of Zebrafish Embryos and Effects of 2,4-Dinitrophenol Exposure

et al. 2015

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Morphology and physiology of fish embryos undergo dramatic changes during their development until the onset of feeding, supplied only by endogenous yolk reserves. For obtaining an insight how these restructuring processes are reflected by body mass related parameters, dry weights (dw), contents of the elements carbon and nitrogen and lipid and protein levels were quantified in different stages within the first four days of embryo development of the zebrafish (Danio rerio). The data show age dependent changes in tissue composition. Dry weights decreased significantly from 79μgdw/egg at 0hours post fertilization (hpf) to 61 μgdw/egg after 96 hpf. The amounts of total carbon fluctuated between 460 mg g-1 and 540 mg g-1 dw, nitrogen was at about 100 mg g-1 dw and total fatty acids were between 48–73 mg g-1 dw. In contrast to these parameters that remained relatively constant, the protein content, which was 240 mg g-1 at 0 hpf, showed an overall increase of about 40%. Comparisons of intact eggs and dechorionated embryos at stages prior to hatching (24, 30, 48 hpf) showed that the differences seen for dry weight and for carbon and nitrogen contents became smaller at more advanced stages, consistent with transition of material from the chorion to embryo tissue. Further, we determined the effect of 2,4-dinitrophenol at a subacutely toxic concentration (14 μM, LC10) as a model chemical challenge on the examined body mass related parameters. The compound caused significant decreases in phospholipid and glycolipid fatty acid contents along with a decrease in the phospholipid fatty acid unsaturation index. No major changes were observed for the other examined parameters. Lipidomic studies as performed here may thus be useful for determining subacute effects of lipophilic organic compounds on lipid metabolism and on cellular membranes of zebrafish embryos.

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Section: Introductionmentioning

confidence: 99%

Body Mass Parameters, Lipid Profiles and Protein Contents of Zebrafish Embryos and Effects of 2,4-Dinitrophenol Exposure

et al. 2015

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“…Then, qPCR was conducted using primer pairs E1F2/E2R and β-actin -F/ β-actin -R. All of qPCR experiments were conducted with RNA extracts from three independent batches of embryos and each reaction was run in triplicate. The expression of β-actin was used as the reference to calculate the relative expression of EGFP or skor2 using the 2 –(ΔΔ Ct) method [ 28 ].…”

Section: Methodsmentioning

confidence: 99%

Generation of an Enhancer-Trapping Vector for Insertional Mutagenesis in Zebrafish

et al. 2015

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Enhancer trapping (ET) is a powerful approach to establish tissue- or cell-specific reporters and identify expression patterns of uncharacterized genes. Although a number of enhancer-trapping vectors have been developed and a large library of fish lines with distinct tissue- or cell-specific expression of reporter genes have been generated, the specificity and efficiency of trapping vectors need to be improved because of the bias interaction of minimal promoters with genomic enhancers. Accordingly, we generated an enhancer-trapping vector pTME that contains a minimal mouse metallothionein gene (mMTI) promoter upstream of EGFP reporter. In the first round of screening, twelve zebrafish lines that carry a single copy of ET cassettes were characterized to have tissue- or cell-specific EGFP expression. One of the highly conserved noncoding elements near an insertion site of trapping cassettes was characterized as an enhancer that can specifically regulate the expression of EGFP in cells of the central nervous system. In addition, the pTME vector contains a mutation-cassette that is able to effectively block the transcription of an endogenous gene in an ET line with ubiquitous EGFP expression. Thus, the pTME vector can be used as an alternative tool for both enhancer trapping and mutagenesis across a target genome.

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“…However, for majority of AS, functional mechanism and relationship to the overlapping protein-coding transcript during development remains largely unclear. Previous transcriptomics studies have identified large number of lncRNAs during embryonic development in vertebrates such as zebrafish (7)(8)(9). Pauli et al, e.g., identified 1133 lncRNAs across eight stages of zebrafish development, out of these 397 were intergenic lncRNAs, 184 intronic overlapping lncRNAs and the rest 566 were classified as exonic overlapping antisense lncRNAs (8).…”

Section: Introductionmentioning

confidence: 99%

Antisense ncRNAs during early vertebrate development are divided in groups with distinct features

Sanjana

Takahashi²,

Carninci

et al. 2020

Preprint

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Long non-coding RNAs or lncRNAs are a broad class of non-protein coding RNAs that are >200nucleotides in length. A number of lncRNAs are shown to play an important role in gene expression regulation. LncRNAs antisense to a protein-coding gene can act either as positive or negative regulators of overlapping protein-coding mRNAs. Almost 50% of lncRNAs present during development of vertebrates such as zebrafish are of antisense lncRNA class. However, their role in gene expression regulation during development remains enigmatic. To understand the role of antisense lncRNAs in early vertebrate development, we took a computational biology approach to analyze existing as well as novel dataset. Our analysis of RNA sequencing data from zebrafish development indicates that antisense RNAs can be divided into two major classes based on their positive or negative co-expression patterns to the sense protein-coding genes. The ones with negative co-expression patterns or group-1 are maternal antisense lncRNAs that overlap mainly developmental genes. Group-2 with positive expression pattern overlap mainly house-keeping genes.Group-1 antisense lncRNAs are longer and more stable as compared to antisense lncRNAs in group-2. In addition, to answer if antisense RNAs in the two groups are differently localized in cell compartments, we deep-sequenced RNA from cytoplasmic and nuclear compartments during early developmental stages. The analysis of these compartment specific datasets revealed group-1 lncRNAs are cytosolic. Based on the cytosolic nature of group-1 RNAs and their higher complementarity to the overlapping developmental mRNAs, we speculate that the group-1 RNAs might function similar to microRNAs in silencing spurious expression of developmental genes. Group-1 and group-2 RNAs are also distinct in terms of their genomic configuration, conservation, length and transcriptional regulation. These results are not only important in understanding the role of antisense RNAs in development but also for predicting the nature of association between antisense lncRNA and overlapping protein-coding genes. ACCESSION NUMBERSThe RNA-seq and CAGE-seq data generated in this study is deposited in GEO database under accession numbers GSE143208 and GSE144040 respectively. SUPPLEMENTARY DATASupplementary Data are available online. ACKNOWLEDGEMENTWe thank Prof Ferenc Mueller and his lab for useful discussions and help with zebrafish methods.We are grateful to all members of ZENCODE ITN for critical comments on the work. We also thank

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Short Stories on Zebrafish Long Noncoding RNAs

Cited by 24 publications

References 87 publications

Body Mass Parameters, Lipid Profiles and Protein Contents of Zebrafish Embryos and Effects of 2,4-Dinitrophenol Exposure

Body Mass Parameters, Lipid Profiles and Protein Contents of Zebrafish Embryos and Effects of 2,4-Dinitrophenol Exposure

Generation of an Enhancer-Trapping Vector for Insertional Mutagenesis in Zebrafish

Antisense ncRNAs during early vertebrate development are divided in groups with distinct features

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