A comparative study of ryanodine receptor (RyR) gene expression levels in a basal ray-finned fish, bichir (Polypterus ornatipinnis) and the derived euteleost zebrafish (Danio rerio)

Darbandi, Siavash Fazel; Franck, Jens P.C.

doi:10.1016/j.cbpb.2009.09.003

Cited by 30 publications

(31 citation statements)

References 23 publications

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“…This includes a previously undescribed RyR3 gene, RyR3b, found in the zebrafish genome. These findings are in contrast to that outlined in previous studies (Darbandi and Franck, 2009; Wu et al, 2011). Darbandi and Franck (2009) suggested that only RyR1 in zebrafish displayed an a and b paralog.…”

Section: Discussioncontrasting

confidence: 99%

“…These findings are in contrast to that outlined in previous studies (Darbandi and Franck, 2009; Wu et al, 2011). Darbandi and Franck (2009) suggested that only RyR1 in zebrafish displayed an a and b paralog. They suggested that the RyR1 duplication took place prior to the teleost whole genome duplication (tWGD) because they showed that bichir ( Polypterus ornatipinnis ), a basal ray finned fish, also possess an RyR1a and an RyR1b with only one RyR2 and one RyR3.…”

Section: Discussioncontrasting

confidence: 99%

“…However, NDL PCBs may display different efficacy and potency in teleosts as compared to mammals, which raises mechanistic questions. In particular, teleosts have at least five RyR genes that display tissue and developmental stage-specific expression (Darbandi and Franck, 2009; Wu et al, 2011). Much less is known about FKBP1 in fish, but zebrafish ( Danio rerio ) have at least three FKBP1 genes (www.zfin.org; Somarelli and Herrera, 2007)), which may contribute to variable NDL PCB toxicity.…”

Section: Introductionmentioning

confidence: 99%

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Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison

et al. 2017

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Non-dioxin-like polychlorinated biphenyls (NDL PCBs) activate ryanodine receptors (RyR), microsomal Ca2+ channels of broad significance. Teleost fish may be important models for NDL PCB neurotoxicity, and we used sequencing databases to characterize teleost RyR and FK506 binding protein 12 or 12.6 kDa (genes FKBP1A; FKBP1B), which promote NDL PCB-triggered Ca2+ dysregulation. Particular focus was placed on describing genes in the Atlantic killifish (Fundulus heteroclitus) genome and searching available RNA-sequencing datasets for single nucleotide variants (SNV) between PCB tolerant killifish from New Bedford Harbor (NBH) versus sensitive killifish from Scorton Creek (SC), MA. Consistent with the teleost whole genome duplication (tWGD), killifish have six RyR genes, corresponding to a and b paralogs of mammalian RyR1, 2 and 3. The presence of six RyR genes was consistent in all teleosts investigated including zebrafish. Killifish have four FKBP1; one FKBP1b and three FKBP1a named FKBP1aa, FKBP1ab, likely from the tWGD and a single gene duplicate FKBP1a3 suggested to have arisen in Atherinomorphae. The RyR and FKBP1 genes displayed tissue and developmental stage-specific mRNA expression, and the previously uncharacterized RyR3, herein named RyR3b, and all FKBP1 genes were prominent in brain. We identified a SNV in RyR3b encoding missense mutation E1458D. In NBH killifish, 57% were heterozygous and 28% were homozygous for this SNV, whereas almost all SC killifish (94%) lacked the variant (n≥39 per population). The outlined sequence differences between mammalian and teleost RyR and FKBP1 together with outlined population differences in SNV frequency may contribute to our understanding of NDL PCB neurotoxicity.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison

et al. 2017

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“…The so called brain RyR isoform, RyR3, which has been demonstrated to occur in skeletal muscle of fish (O'Brien et al, 1995; Darbandi and Franck, 2009), displayed high variability in NBH killifish skeletal muscle, and the expression levels were not different from levels found in SC killifish. Levels of cav1.1 , the L-type Ca 2+ channel, α subunit of isoform 1, which mechanically interacts with the RyR1 to drive excitation contraction (EC) coupling in skeletal muscle, also were consistent between killifish from the two populations.…”

Section: 0 Results and Discussionmentioning

confidence: 96%

Expression and function of ryanodine receptor related pathways in PCB tolerant Atlantic killifish (Fundulus heteroclitus) from New Bedford Harbor, MA, USA

et al. 2015

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Atlantic killifish (Fundulus heteroclitus) thrive in New Bedford Harbor (NBH), MA, highly contaminated with polychlorinated biphenyls (PCBs). Resident killifish have evolved tolerance to dioxin-like (DL) PCBs, whose toxic effects through the aryl hydrocarbon receptor (AhR) are well studied. In NBH, non-dioxin like PCBs (NDL PCBs), which lack activity toward the AhR, vastly exceed levels of DL congeners yet how killifish counter NDL toxic effects has not been explored. In mammals and fish, NDL PCBs are potent activators of ryanodine receptors (RyR), Ca2+ release channels necessary for a vast array of physiological processes. In the current study we compared the expression and function of RyR related pathways in NBH killifish with killifish from the reference site at Scorton Creek (SC, MA). Relative to the SC fish, adults from NBH displayed increased levels of skeletal muscle RyR1 protein, and increased levels of FK506-binding protein 12 kDa (FKBP12), an accessory protein essential for NDL PCB-triggered changes in RyR channel function. In accordance with increased RyR1 levels, NBH killifish displayed increased maximal ligand binding, increased maximal response to Ca2+ activation and increased maximal response to activation by the NDL PCB congener PCB 95. Compared to SC, NBH embryos and larvae had increased levels of mtor and ryr2 transcripts at multiple stages of development, and generations, while levels of serca2 were decreased at 9 days post-fertilization in the F1 and F2 generations. These findings suggest that there are compensatory and heritable changes in RyR mediated Ca2+ signaling proteins or potential signaling partners in NBH killifish.

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“…Genespecific primers for high-confidence ASD genes and the Eif1a housekeeping gene (HKG) were designed using the Primer3 program (Supplemental Table S7; Rozen and Skaletsky 2000). The expression levels of the target genes were normalized relative to the expression levels of Eif1a HKG, and then expression levels between Tbr1-knockouts and wild-type littermates were compared as previously described (Pfaffl 2001;Darbandi and Franck 2009). …”

Section: Quantitative Real-time Pcr (Qrt-pcr)mentioning

confidence: 99%

TBR1 regulates autism risk genes in the developing neocortex

et al. 2016

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Exome sequencing studies have identified multiple genes harboring de novo loss-of-function (LoF) variants in individuals with autism spectrum disorders (ASD), including TBR1, a master regulator of cortical development. We performed ChIPseq for TBR1 during mouse cortical neurogenesis and show that TBR1-bound regions are enriched adjacent to ASD genes. ASD genes were also enriched among genes that are differentially expressed in Tbr1 knockouts, which together with the ChIP-seq data, suggests direct transcriptional regulation. Of the nine ASD genes examined, seven were misexpressed in the cortices of Tbr1 knockout mice, including six with increased expression in the deep cortical layers. ASD genes with adjacent cortical TBR1 ChIP-seq peaks also showed unusually low levels of LoF mutations in a reference human population and among Icelanders. We then leveraged TBR1 binding to identify an appealing subset of candidate ASD genes. Our findings highlight a TBR1-regulated network of ASD genes in the developing neocortex that are relatively intolerant to LoF mutations, indicating that these genes may play critical roles in normal cortical development.

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A comparative study of ryanodine receptor (RyR) gene expression levels in a basal ray-finned fish, bichir (Polypterus ornatipinnis) and the derived euteleost zebrafish (Danio rerio)

Cited by 30 publications

References 23 publications

Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison

Ryanodine receptor and FK506 binding protein 1 in the Atlantic killifish (Fundulus heteroclitus): A phylogenetic and population-based comparison

Expression and function of ryanodine receptor related pathways in PCB tolerant Atlantic killifish (Fundulus heteroclitus) from New Bedford Harbor, MA, USA

TBR1 regulates autism risk genes in the developing neocortex

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