Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells

Gene. 2007 Jan 15;386(1-2):11-23. doi: 10.1016/j.gene.2006.07.023. Epub 2006 Aug 5.


Hair cells express a complement of ion channels, representing shared and distinct channels that confer distinct electrophysiological signatures for each cell. This diversity is generated by the use of alternative splicing in the alpha subunit, formation of heterotetrameric channels, and combinatorial association with beta subunits. These channels are thought to play a role in the tonotopic gradient observed in the mammalian cochlea. Mouse Kcnma1 transcripts, 5' and 3' ESTs, and genomic sequences were examined for the utilization of alternative splicing in the mouse transcriptome. Comparative genomic analyses investigated the conservation of KCNMA1 splice sites. Genomes of mouse, rat, human, opossum, chicken, frog and zebrafish established that the exon-intron structure and mechanism of KCNMA1 alternative splicing were highly conserved with 6-7 splice sites being utilized. The murine Kcnma1 utilized 6 out of 7 potential splice sites. RT-PCR experiments using murine gene-specific oligonucleotide primers analyzed the scope and variety of Kcnma1 and Kcnmb1-4 expression profiles in the cochlea and inner ear hair cells. In the cochlea splice variants were present representing sites 3, 4, 6, and 7, while site 1 was insertionless and site 2 utilized only exon 10. However, site 5 was not present. Detection of KCNMA1 transcripts and protein exhibited a quantitative longitudinal gradient with a reciprocal gradient found between inner and outer hair cells. Differential expression was also observed in the usage of the long form of the carboxy-terminus tail. These results suggest that a diversity of splice variants exist in rodent cochlear hair cells and this diversity is similar to that observed for non-mammalian vertebrate hair cells, such as chicken and turtle.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics
  • Animals
  • Conserved Sequence
  • Gene Expression Profiling*
  • Genetic Variation*
  • Hair Cells, Auditory, Inner / metabolism*
  • Humans
  • In Situ Hybridization
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits / biosynthesis
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits / genetics*
  • Mice
  • Rats
  • Transcription, Genetic*


  • KCNMA1 protein, human
  • Kcnma1 protein, mouse
  • Kcnma1 protein, rat
  • Large-Conductance Calcium-Activated Potassium Channel alpha Subunits