Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA.
J Assoc Res Otolaryngol. 2011 Aug;12(4):423-35. doi: 10.1007/s10162-011-0259-2. Epub 2011 Mar 12.
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.
在禽类听觉上皮的音调拓扑轴——基底乳头（BP）中，毛细胞的特性存在已知差异。为了确定这些差异的遗传基础，我们比较了 0 日龄雏鸡听觉上皮的高频（HF）、中频和低频（LF）三分之一部分的基因表达。从每个样本中扩增的 RNA 与全基因组鸡芯片杂交，并用 GeneSpring 软件来识别差异表达的基因。使用 2 倍的折叠变化和 0.05 的 p 值作为截止值，在 HF 和 LF 段之间发现了 2663 个差异表达的基因。许多离子通道基因在 BP 的 HF 和 LF 区域之间表现出差异表达，这种表达模式在以前的研究中已经在部分但不是所有这些基因中得到了证实。定量 PCR 用于验证 15 个基因（包括 KCNMA1（Slo）及其交替剪接的 STREX 外显子）在音调上的表达。对微阵列数据进行了基因集富集分析（GSEA），结果显示许多 miRNA 基因集在 HF 段相对 LF 段显著富集，表明存在音调活性梯度。GSEA 还表明，蛋白激酶 C 和蛋白激酶 A 的激酶在 HF 和 LF 端的活性存在差异，这与 STREX 外显子在音调上的表达使 Slo 对激酶的活性敏感的观察结果相吻合，这是一个有趣的推论。综上所述，这些结果表明了诱导和维持音调性的机制，并增强了我们对鸡 BP 中近端-远端基因表达梯度的复杂性质的理解。
