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BMC Res Notes 2015 Nov 18;8:691. doi: 10.1186/s13104-015-1485-1.
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RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM(®) genes for hereditary disorders of hearing and balance.

Ramírez-Gordillo D , Powers TR , van Velkinburgh JC , Trujillo-Provencio C , Schilkey F , Serrano EE .

Auditory 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. Using Affymetrix GeneChip(®) X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus laevis 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. As 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.

PubMed ID: 26582541
PMC ID: PMC4652436
Article link: BMC Res Notes
Grant support: [+]

Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: acta1 actb adcy1 aldh7a1 atoh1 atp2b4 bsnd ccdc50 cdh23 cemip cib2 clic5 clrn1 coch col2a1 crym elmod3 eps8 espn f2 foxi1 gipc3 gjb2 grxcr1 grxcr2 hoxa1 ildr1 jag1 kars1 kcnj10 kcnq4 lhfpl5 loxhd1 lrtomt marveld2 mcoln3 msrb3 myh14 myo15a myo3a myo7a otoa otof otogl2 otop1 otor pcdh15 pdzd7 pjvk pou3f3 pou3f4 ptprq rdx serpinb6 slc26a4.3 slitrk6 strc tbx1 tjp2 tmc1 tmc2 tmie tmprss3 tspear ush1c ush1g ush2a whrn
GO keywords: vestibulocochlear nerve development

Disease Ontology terms: nonsyndromic deafness [+]
GEO Series: GSE69701: Xenbase,  NCBI
GSE73829: NCBI

Article Images: [+] show captions
References [+] :
Agrawal, Disorders of balance and vestibular function in US adults: data from the National Health and Nutrition Examination Survey, 2001-2004. 2009, Pubmed