Researchers at the University of Rochester Medical Center report on results from a targeted splice sequencing study of myotonic dystrophy type 1 (DM1) in a mouse model of the dominantly inherited neuromuscular disease. In mice carrying characteristic CUG repeat expansions or missing members of the "muscleblind-like" (Mbnl) splicing factors, the team saw alternative splicing shifts in mouse muscle tissue transcriptomes, prompting the investigators to take a closer look at nearly three dozen dysregulated exons using targeted RNA sequencing. On the other hand, by targeting the CUG repeats with antisense therapeutic oligonucleotides, the authors note found that they could dial down myotonia in the mice, while starting to restore alternative splicing. "Taken together," they write, "these results indicate that targeted RNA splice sequencing provides a reliable indicator of RNA toxicity that responds rapidly to treatment."
A team from the University of California, Davis, presents a structural variant (SV) genotyping tool called Nebula, based on predictions done with k-mer data from whole-genome sequencing reads rather than breakpoint mapping. "We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches," the researchers say, noting that Nebula compares favorably to available mapping-based SV genotyping methods when it comes to speed with similar accuracy. "We have demonstrated that k-mers can act as a lightweight and simple alternative for expansive mapping-based methods to genotype polymorphic SVs," they write, adding that "extending Nebula to utilize k-mers that are shared between different SVs may help us improve our performance when genotyping SVs in repeat regions of the genome (e.g. tandem repeats)."
Investigators from Belgium and the US outline an in situ assay for visualizing epigenetic marks with the help of biochemical tagging and targeted microscopy. The team's "epigenetic visualization assay" (EVA) involves the use of antibody-conjugated alkaline phosphatase enzymes and phosphorylated fluorophore-labeled DNA oligonucleotides to label 5-methylcytosine, histone acetylation marks, or other epigenetic modifiers. The EVA approach "is based on an in situ proximity reaction that generates fluorescent signal proportional to the density of an epigenetic mark as DNA methylation or histone modifications at the gene of interest," the authors say, noting that the assay can be combined with RNA fluorescence in situ hybridization to track DNA methylation and RNA transcription in tandem.