Probing the Xenopus laevis inner ear transcriptome for biological function

Powers, TuShun R.; Virk, Selene; Trujillo-Provencio, Casilda; Serrano, Elba E.

doi:10.1186/1471-2164-13-225

Cited by 11 publications

(14 citation statements)

References 77 publications

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“…As expected, Eya and Gro have the highest interaction scores, but several other proteins were identified as potential co-factors. We took advantage of this data set to screen for potential vertebrate Six1 co-factors using Xenopus , a tetrapod that has highly homologous middle/inner ear gene expression, morphology and hearing characteristics compared to humans (Elepfandt et al, 2000; Mason et al, 2009; Powers et al, 2012; Quick and Serrano, 2005; Schoffelen et al, 2008; van Dijk et al, 2011). Because the amino acid sequence of the SD of fly SO is highly conserved in vertebrate Six1 and the frog SD amino acid sequence is identical to human (Fig.…”

Section: Introductionmentioning

confidence: 99%

Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development

Neilson

Abbruzzesse

Kenyon

et al. 2017

Developmental Biology

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Mutations in SIX1 and in its co-factor, EYA1, underlie Branchiootorenal Spectrum disorder (BOS), which is characterized by variable branchial arch, otic and kidney malformations. However, mutations in these two genes are identified in only half of patients. We screened for other potential co-factors, and herein characterize one of them, Pa2G4 (aka Ebp1/Plfap). In human embryonic kidney cells, Pa2G4 binds to Six1 and interferes with the Six1-Eya1 complex. In Xenopus embryos, knock-down of Pa2G4 leads to down-regulation of neural border zone, neural crest and cranial placode genes, and concomitant expansion of neural plate genes. Gain-of-function leads to a broader neural border zone, expanded neural crest and altered cranial placode domains. In loss-of-function assays, the later developing otocyst is reduced in size, which impacts gene expression. In contrast, the size of the otocyst in gain-of-function assays is not changed but the expression domains of several otocyst genes are reduced. Together these findings establish an interaction between Pa2G4 and Six1, and demonstrate that it has an important role in the development of tissues affected in BOS. Thereby, we suggest that pa2g4 is a potential candidate gene for BOS.

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Section: Introductionmentioning

confidence: 99%

Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development

Neilson

Abbruzzesse

Kenyon

et al. 2017

Developmental Biology

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“…Myosin VIA , otolin-1 , SPARC3 , and otogelin expression was also verified by RT-PCR. Microarray-based transcriptome profiling has identified many of these so-called deafness genes in the ears of other vertebrates, including rodents and the aquatic frog Xenopus [ 17 , 19 , 20 ].…”

Section: Discussionmentioning

confidence: 99%

Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes

Faber-Hammond

Samanta²,

Whitchurch

et al. 2015

PLoS ONE

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Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males) collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well as a range of future midshipman and cross-species comparative studies of the auditory periphery.

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“…Fifty-one percent of reads aligned to the X. tropicalis reference genome. The microarray procedures and data were processed as previously described [ 17 ]. Data from three biological replicates were preprocessed using Gene Chip robust multichip averaging (GCRMA) to generate a log 2 transformed intensity measure for each Xl-PSID.…”

Section: Methodsmentioning

confidence: 99%

“…Understanding of the genetic underpinnings of hearing and balance common to Xenopus and humans can be furthered by using high throughput approaches to profile the cadre of genes whose collective expression is required in a functioning inner ear organ [ 16 , 17 ]. To this end we used bioinformatics tools, in combination with microarrays and RNA-Seq, to determine whether Online Mendelian Inheritance in Man ® (OMIM ® ) orthologues for hearing and balance are expressed in the Xenopus inner ear.…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance

et al. 2015

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BackgroundAuditory and vestibular disorders are prevalent sensory disabilities caused by genetic and environmental (noise, trauma, chemicals) factors that often damage mechanosensory hair cells of the inner ear. Development of treatments for inner ear disorders of hearing and balance relies on the use of animal models such as fish, amphibians, reptiles, birds, and non-human mammals. Here, we aimed to augment the utility of the genus Xenopus for uncovering genetic mechanisms essential for the maintenance of inner ear structure and function.ResultsUsing Affymetrix GeneChip®X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopuslaevis inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies demonstrated that, with our methods, a combination of microarray and RNA-Seq detected expression of more genes than either platform alone.ConclusionsAs part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used to investigate hearing and balance using genetic and informatics procedures that are available through the National Xenopus Resource (NXR), and the open access data repository, Xenbase. The results and approaches presented here expand the viability of Xenopus as an animal model for inner ear research.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1485-1) contains supplementary material, which is available to authorized users.

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Probing the Xenopus laevis inner ear transcriptome for biological function

Cited by 11 publications

References 77 publications

Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development

Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development

Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes

RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance

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