It’s been nearly two years since a team of scientists from the University of California, Davis, School of Medicine published the first-ever complete sequence of FMR1, the gene associated with a repeat expansion that causes Fragile X syndrome. That team is once again breaking new ground, this time characterizing alternative splicing and full-length transcripts of FMR1. For both studies, the scientists relied on Single Molecule, Real-Time (SMRT®) Sequencing because its uniquely long reads allowed them to span the gene and generate sequence and isoform data that would not have been possible any other way.
The new paper, “Differential increases of specific FMR1 mRNA isoforms in premutation carriers,” was published in the Journal of Medical Genetics and comes from lead author Dalyir Pretto and senior author Flora Tassone, along with collaborators. They aimed to elucidate the transcript levels of FMR1 in people with what’s known as a premutation allele — people who have more repeats within the FMR1 gene than normal, but fewer repeats than full-mutation Fragile X patients have. This group is at risk for fragile X-associated tremor/ataxia syndrome as well as fragile X-associated primary ovarian insufficiency.
Earlier studies using qRT-PCR had found significant levels of alternative splicing in FMR1, but “PCR-based methodologies only allow the individual splice sites to be analysed separately and therefore fail to provide the combinations of different splice sites within the same RNA molecule,” Pretto et al. report. “Our approach, which has used the single-molecule long-read sequencing technology, has allowed us to obtain a transcript map of all of the splice combinations within a single FMR1 transcript, and more importantly in both premutation and control individuals.” Their goal was to quantify isoforms to understand their role in pathogenesis for disorders associated with premutation carriers.
The authors’ findings included some unexpected results. For example, they detected alternative splicing around exon 3 of FMR1, a region where splicing had not previously been found or even predicted. They also found that only two of the 17 exons had alternative start sites. Overall, they noted that while “the relative abundance of all mRNA isoforms was significantly increased in the premutation group,” two particular isoforms were most increased, indicating possible functional relevance for premutation disorder pathology.
As these represent the first comprehensive transcript findings for the FMR1 gene, the scientists underscore the need for future studies to more fully characterize the downstream effects of the transcripts they sequenced.