Characterization of Tissue-Specific and Developmentally Regulated Alternative Splicing of Exon 64 in theCOL5A1Gene

Abstract

The COL5A1 gene, a member of the clade B fibrillar collagen gene family, was recently shown to contain two alternatively spliced exons (64A and 64B) that encode 23 amino acids in the carboxyl-terminal propeptide. The two are identical in length, very similar in sequence, and used in a mutually exclusive fashion because of the small intron that separates them. Each COL5A1 allele uses both exons, but a given transcript will contain only one of the two exons. The sequences in other species are highly conserved at the amino acid level. The expression profile of the two isoforms was determined from analysis of RNA levels in a panel of murine tissues. While both isoforms were found in all tissues studied, actively proliferating tissues (liver, lung) used isoform B more often, while a less mitotically-active tissue, brain, had a higher proportion of exon 64A. The high degree of conservation between the two exons is consistent with a regional genomic duplication. The presence of the two isoforms as far back as pufferfish (tetraodon) implies an important functional significance. The exact role determined by the two sequences is not known, but involvement in the determination of chain composition of mature type V collagen or regulation of cell activity are possible, given the differences in tissue distribution.

Integrated Transcriptome and Network Analysis Reveals Spatiotemporal Dynamics of Calvarial Suturogenesis

“…Notable examples included Col5a1 and Postn . The tendon marker Col5a1 encodes the alpha 1 chain of type V collagen, and the SM showed increased expression of isoforms containing exon 64A with a concomitant decrease in exon 64B at E16.5 and E18.5, potentially altering a C-terminal fibrillar collagen domain that may be involved in substrate binding ( Mitchell et al, 2012 ) ( Figure 2D ). Postn encodes periostin, a secreted ECM protein that is a key regulator of cell behavior and ECM organization ( Bonnet et al, 2016 ).…”

“…Mutations of Col5a1 cause Ehlers-Danlos syndrome, a collagenopathy with joint hypermobility, skin hyperelasticity, and tissue fragility with atrophic scarring ( Malfait and De Paepe, 2014 ). Alternative exons 64A and 64B may modify the specificity of the collagen chain selectivity recognition domain encoded by exon 65 ( Mitchell et al, 2012 ). Interestingly, exon 64B is used most frequently in actively proliferating tissue ( Mitchell et al, 2012 ), and in our data, exon 64B was enriched in the more proliferative OFs compared to SM.…”

The alternatively spliced exon of COL5A1 is mutated in autosomal recessive classical Ehlers‐Danlos syndrome

“…Transcription of COL5A1 is unusual in that there are two mutually exclusive exons (64a and 64b) that are both transcribed by each allele but are alternatively spliced in the resulting two mature isoforms (isoform a and b, respectively). 3 This genomic arrangement is highly conserved across many species, which suggests an important functional role. One hypothesis is that the binary choice between 64a and 64b confers specificity to the chain selectivity recognition domain encoded in exon 65.…”

“…One hypothesis is that the binary choice between 64a and 64b confers specificity to the chain selectivity recognition domain encoded in exon 65. 3 Despite the many reported pathogenic variants in COL5A1, none has been encountered in 64a or 64b prompting some to predict that such variants must result in an atypical phenotype. 3 Here, we confirm this prediction by showing that a homozygous truncating variant in 64b results in the first known case of autosomal recessive COL5A1-related cEDS.…”

“…The reported dynamic difference in abundance between these 2 transcripts suggests that the apparent sparing of isoform a allowed the carrier parents to compensate, especially since isoform b only accounts for <30% of COL5A1 in skin and knees. 3 It will be of interest to observe the clinical consequence of pathogenic variants in exon 64a in humans and their mode of inheritance.…”