Gene expression gradients along the tonotopic axis of the chicken auditory epithelium

J Assoc Res Otolaryngol. 2011 Aug;12(4):423-35. doi: 10.1007/s10162-011-0259-2. Epub 2011 Mar 12.

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 low-frequency (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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Animals, Newborn / metabolism*
  • Calcium Channels / genetics
  • Calcium Channels / metabolism
  • Chickens
  • Cyclic AMP-Dependent Protein Kinases / genetics
  • Cyclic AMP-Dependent Protein Kinases / metabolism
  • Gene Expression Profiling*
  • Gene Expression Regulation, Developmental / physiology*
  • Hair Cells, Auditory / metabolism*
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits / genetics
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits / metabolism
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • Models, Animal
  • Organ of Corti / metabolism*
  • Protein Kinase C / genetics
  • Protein Kinase C / metabolism
  • Sodium Channels / genetics
  • Sodium Channels / metabolism

Substances

  • Calcium Channels
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits
  • MicroRNAs
  • Sodium Channels
  • Cyclic AMP-Dependent Protein Kinases
  • Protein Kinase C