Characterisation of CDKL5 Transcript Isoforms in Human and Mouse

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.

Characterisation of Cdkl5 transcript isoforms in rat

“…2). This also reflects the pattern of expression seen in mouse and human (Hector et al, 2016). Of the two isoforms expressed in the brain, rCdkl5_1 is the major isoform, as detected by qRT-PCR (Fig.…”

“…rCdkl5_1 is expressed most abundantly within the brain, but is also detected in all of the adult tissues tested, showing a similar pattern of expression to that of the mouse, and human ( Fig. 2) (Hector et al, 2016). rCdkl5_2, which incorporates the highly conserved exon 17, is also expressed primarily in the brain, but can only be detected at lower levels in some other peripheral tissues (Fig.…”

“…Bioinformatic and molecular analyses were performed as described previously to investigate the transcript isoforms of rat Cdkl5 (Hector et al, 2016). In brief, RNA-seq datasets were analysed (rat brain GEO sample ID's GSM1020666, GSM1020675 and GSM1020684; rat testis GEO sample ID's GSM1020674, GSM1020683, GSM1020692 (Merkin et al, 2012)) and mapped to the rat genome using the STAR read aligner, version 2.4.2a.…”

“…1A, Table 1). In accordance with new nomenclature recommendations (Hector et al, 2016), we have named these rCdkl5_1, rCdkl5_2, rCdkl5_9, and rCdkl5_10. The composition of each transcript, the exon boundaries and chromosomal sequence coordinates are detailed in Table 2. RNA-seq analysis also predicted two rare transcripts containing additional exons that were detected and confirmed by sequencing of RT-PCR amplicons (data not shown).…”

“…In a recent study we characterised the structure of the human CDKL5 and mouse Cdkl5 genes, identifying a number of transcript isoforms resulting from alternative splicing (Hector et al, 2016). In the rat, two different transcript isoforms have been identified to date; CDKL5a and CDKL5b (GenBank accession numbers FJ807484 and GU351881, respectively) (Chen et al, 2010).…”