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Updated: Jan 22, 2026
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
Published on: July 7, 2010
Common tissue-specific expressions and regulatory factors of c-KIT isoforms with and without GNNK and GNSK sequences
Rikuto Goto1, Naoaki Sakamoto1,2, Akinori Awazu1,2
1Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan.
Abstract:
c-KIT is a transmembrane receptor tyrosine kinase involved in various signaling pathways. Alternative pre-mRNA splicing of KIT results in isoforms that differ in the presence or absence of four amino acid sequences in the extracellular juxtamembrane region, such as, isoforms with and without the GNNK sequence (GNNK+ and GNNK - , respectively) in humans and mice, and those with and without GNSK (GNSK+ and GNSK - , respectively) in domestic dogs, cats, and sheep. These isoforms have been extensively studied as disease-associated (particularly tumors or cancer) splice variants with differing kinase activities. However, the expression patterns and regulatory factors of each isoform in various animal species without tumors or cancer remain poorly understood. Studying these aspects can provide the basis for understanding the associations between c-KIT isoforms and disease. Therefore, in the present study, a comprehensive expression analysis of c-KIT isoforms was conducted using tissue-wide transcriptome data from humans, mice, dogs, cats, and sheep. We found that the expression ratio of c-KIT isoforms differs across tissues, and such features are conserved across animal species: GNNK+ and GNSK+ isoforms have high expression ratios in the central nervous system, while GNNK- and GNSK- predominate in other tissues. Furthermore, NOVA2, RBFOX1, RBFOX3, and DYRK1A were suggested to be candidate factors regulating the selection of the alternative 5' splice donor site of KIT.
Insights
The c-KIT receptor tyrosine kinase has different splice variants, with specific variants predominantly expressed in the central nervous system across multiple species. This finding provides insights into c-KIT isoform regulation and function.
Area of Science:
- Molecular Biology
- Genetics
- Comparative Genomics
Background:
- c-KIT, a receptor tyrosine kinase, plays a role in cell signaling.
- Alternative splicing of KIT generates isoforms with varying amino acid sequences, impacting kinase activity.
- These isoforms are linked to diseases, but their normal expression patterns are unclear.
Purpose of the Study:
- To investigate the expression patterns of c-KIT isoforms across different tissues and animal species.
- To identify potential regulatory factors involved in KIT alternative splicing.
Main Methods:
- Comprehensive analysis of tissue-wide transcriptome data from humans, mice, dogs, cats, and sheep.
- Comparative expression profiling of c-KIT isoforms.
Main Results:
- Expression ratios of c-KIT isoforms vary significantly across tissues.
- A conserved pattern shows GNNK+ and GNSK+ isoforms are highly expressed in the central nervous system.
- GNNK- and GNSK- isoforms are predominant in other tissues.
- NOVA2, RBFOX1, RBFOX3, and DYRK1A are proposed as regulatory factors for KIT splicing.
Conclusions:
- Tissue-specific and conserved expression patterns of c-KIT isoforms exist across species.
- Understanding these patterns is crucial for elucidating the role of c-KIT in health and disease.
- Specific RNA-binding proteins may regulate KIT alternative splicing.
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