Characterisation of CDKL5 Transcript Isoforms in Human and Mouse.

Ralph D Hector,Nicoletta Landsberger,Owen Dando,Peter C Kind,Stuart R Cobb,Mark E S Bailey,Charlotte Kilstrup-Nielsen,Ruben Artero

doi:10.1371/journal.pone.0157758

Abstract

Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene (CDKL5) cause early onset infantile spasms and subsequent severe developmental delay in affected children. Deleterious mutations have been reported to occur throughout the CDKL5 coding region. Several studies point to a complex CDKL5 gene structure in terms of exon usage and transcript expression. Improvements in molecular diagnosis and more extensive research into the neurobiology of CDKL5 and pathophysiology of CDKL5 disorders necessitate an updated analysis of the gene. In this study, we have analysed human and mouse CDKL5 transcript patterns both bioinformatically and experimentally. We have characterised the predominant brain isoform of CDKL5, a 9.7 kb transcript comprised of 18 exons with a large 6.6 kb 3’-untranslated region (UTR), which we name hCDKL5_1. In addition we describe new exonic regions and a range of novel splice and UTR isoforms. This has enabled the description of an updated gene model in both species and a standardised nomenclature system for CDKL5 transcripts. Profiling revealed tissue- and brain development stage-specific differences in expression between transcript isoforms. These findings provide an essential backdrop for the diagnosis of CDKL5-related disorders, for investigations into the basic biology of this gene and its protein products, and for the rational design of gene-based and molecular therapies for these disorders.

Highlights

Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene, CDKL5 (Mendelian Inheritance in Man, MIM: 300203; previously known as STK9), cause a range of phenotypes, including EIEE2 (MIM: 300672), a form of early infantile epileptic encephalopathy [1, 2], and infantile spasms [3,4,5,6,7]
The combined RNA-seq and RT-PCR data demonstrated the existence of five major transcript isoforms containing distinct coding regions, which we have termed hCDKL5_1 to hCDKL5_5 (Fig 1; see nomenclature recommendations section below)
CDKL5 disorder is a rare, debilitating form of early infantile epileptic encephalopathy and severe intellectual disability caused by a range of de novo mutations in the CDKL5 gene

Summary

Introduction

Mutations in the X-linked Cyclin-Dependent Kinase-Like 5 gene, CDKL5 (Mendelian Inheritance in Man, MIM: 300203; previously known as STK9), cause a range of phenotypes, including EIEE2 (MIM: 300672), a form of early infantile epileptic encephalopathy [1, 2], and infantile spasms [3,4,5,6,7]. It is widely assumed that most CDKL5-related phenotypes result from loss of function mutations, but putative gain-of-function mutations [12], as well as large duplication events that include the CDKL5 gene region, have been identified [13,14,15]

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Conclusion