Gene Expression Gradients along the Tonotopic Axis of the Chicken Auditory Epithelium

Abstract

There are known differences in the properties of hair cells along the tonotopic axis of the avian auditory epithelium, the basilar papilla (BP). To determine the genetic basis of these differences, we compared gene expression between the high-(HF), middle-, and lowfrequency (LF) thirds of 0-day-old chick auditory epithelia. RNA amplified from each sample was hybridized to whole-genome chicken arrays and GeneSpring software was used to identify differentially expressed genes. Two thousand six hundred sixty-three genes were found to be differentially expressed between the HF and LF segments, using a fold-change cutoff of 2 and a p value of 0.05. Many ion channel genes were differentially expressed between the HF and LF regions of the BP, an expression pattern that was previously established for some but not all of these genes. Quantitative PCR was used to verify tonotopic expression of 15 genes, including KCNMA1 (Slo) and its alternatively spliced STREX exon. Gene set enrichment analyses (GSEA) were performed on the microarray data and revealed many microRNA gene sets significantly enriched in the HF relative to the LF end, suggesting a tonotopic activity gradient. GSEA also suggested differential activity of the kinases protein kinase C and protein kinase A at the HF and LF ends, an interesting corollary to the observation that there is tonotopic expression of the STREX exon that confers on Slo sensitivity to the activity of kinases. Taken together, these results suggest mechanisms of induction and maintenance of tonotopicity and enhance our understanding of the complex nature of proximal-distal gene expression gradients in the chicken BP.

Gradients and Modulation of K+ Channels Optimize Temporal Accuracy in Networks of Auditory Neurons

“…The finding of gradients of expression of ion channels in the central auditory system was preceded by findings of similar gradients in sensory hair cells in the cochlea [52], [53], [54], [55], [56]. In some lower vertebrates, these differences in levels of ion channels in different hair cells serve to tune the electrical responses of the cells to specific sound frequencies [57], [58], [59], [60], [61], [62].…”

Hair cell BK channels interact with RACK1, and PKC increases its expression on the cell surface by indirect phosphorylation

“…CDK5 mediates its effects by direct phosphorylation while the effects of GSK3 phosphorylation are also mediated by interactions with ␤-catenin, which, in turn, promotes Slo surface expression (8,11,43). In other work we have inferred gradients in kinase activity along the tonotopic axis with increasing PKA in low-frequency hair cells and increasing PKC activity in high-frequency hair cells (21). In seeking explanations for the gradients in BK channel surface expression along the tonotopic axis, we identified the WD40 adapter protein receptor for activated PKC (Rack1) as a binding partner of Slo using a yeast two-hybrid screen.…”

“…Currents carried by BK channels and the number of BK channel clusters increase in high-frequency hair cells (7,40). The increase in channel clusters is at variance with the amounts of Slo transcripts that show an opposite decrease in high-frequency hair cells (21,32). The seeming paradox between mRNA and Slo surface expression gradients along the tonotopic axis is likely to be mediated by complex mechanisms.…”

High throughput gene expression analysis of the inner ear

“…Shah et al described the gene expression profile of the modiolus in two-month old wild type mice, and used it to measure the level of the mRNAs of potential neuronal guidance receptors in the adult cochlea (Shah et al, 2009). To address molecular differences that confer tonotopic-organization to the auditory system, a region-specific analysis was performed both in mouse and chicken auditory epithelia comparing gene expression profiles from low frequency and high frequency areas (Frucht et al, 2011;Sato et al, 2009). Finally, Abe et al extracted RNA from a single human adult cochlea and several vestibular systems from patients who underwent labyrinthectomy for non-labyrinthine disorders, and identified CRYM as a highly expressed gene, which they subsequently found to underlie human hereditary non-syndromic hearing loss (Abe et al, 2003).…”