Highly Specific Alternative Splicing of Transcripts Encoding BK Channels in the Chicken's Cochlea Is a Minor Determinant of the Tonotopic Gradient

Abstract

The frequency sensitivity of auditory hair cells in the inner ear varies with their longitudinal position in the sensory epithelium. Among the factors that determine the differential cellular response to sound is the resonance of a hair cell's transmembrane electrical potential, whose frequency correlates with the kinetic properties of the high-conductance Ca²⁺-activated K⁺ (BK) channels encoded by a Slo (kcnma1) gene. It has been proposed that the inclusion of specific alternative axons in the Slo transcripts along the cochlea underlies the gradient of BK-channel kinetics. By analyzing the complete sequences of chicken Slo gene (cSlo) cDNAs from the chicken's cochlea, we show that most transcripts lack alternative exons. Transcripts with more than one alternative exon constitute only 10% of the total. Although the fraction of transcripts containing alternative exons increases from the cochlear base to the apex, the combination of alternative exons is not regulated. There is also a clear increase in the expression of BK transcripts with long carboxyl termini toward the apex. When long and short BK transcripts are expressed in HEK-293 cells, the kinetics of single-channel currents differ only slightly, but they are substantially slowed when the channels are coexpressed with the auxiliary β subunit that occurs more widely at the apex. These results argue that the tonotopic gradient is not established by the selective inclusion of highly specific cSlo exons. Instead, a gradient in the expression of β subunits slows BK channels toward the low-frequency apex of the cochlea.

Supplemental material for this article may be found at http://mcb.asm.org/.

We thank D. Andor-Ardó for assistance with Bayesian statistics; B. Fabella for LabVIEW programming; S. Pylawka, J. Villiers, and M. Vologodskaia for technical assistance; and A. Le Boeuf for comments on the manuscript. We are grateful to D. Betel (Memorial Sloan-Kettering Cancer Center) for help in predicting miRNA targets for the cSlo 3′UTR sequence and to M. Grunnet for discussions about unproductive splicing.

This research was supported by grant DC00241 from the National Institutes of Health and by a Sue and Frank Binswanger Grant in Auditory Science from the National Organization for Hearing Research Foundation. S.M.-R. was supported by an F. M. Kirby Postdoctoral Fellowship; A.J.H. is an Investigator of Howard Hughes Medical Institute.