Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation

The maternal-effect mutation ichabod (ich) results in ventralized zebrafish embryos due to impaired induction of the dorsal canonical Wnt-signaling pathway. While previous studies linked the phenotype to reduced ctnnb2 transcript levels, the causative mutation remained unidentified. Using long-read sequencing, we discovered that the ich phenotype stems from the insertion of a non-autonomous CMC-Enhancer/Suppressor-mutator (CMC-EnSpm) transposon in the 3'UTR of the gene. Through reporter assays, we demonstrate that while wild type ctnnb2 mRNAs exhibit remarkably high stability throughout the early stages of development, the insertion of the transposon dramatically reduces transcript stability. Genome-wide mapping of the CMC-EnSpm transposons across multiple zebrafish strains also indicated ongoing transposition activity in the zebrafish genome. Our findings not only resolve the molecular basis of the ich mutation but also highlight the continuing mutagenic potential of endogenous transposons and reveal unexpected aspects of maternal transcript regulation during early zebrafish development.

Experimental reporting of fish transcriptomic responses in environmental toxicology and ecotoxicology

Due to its increasing affordability and efforts to understand transcriptional responses of organisms to biotic and abiotic stimuli, transcriptomics has become an important tool with significant impact on toxicological investigations and hazard and risk assessments, especially during development and application of new approach methodologies (NAMs). Data generated using transcriptomic methodologies have directly informed adverse outcome pathway frameworks, chemical and biological read across, and aided in the identification of points of departure. Using data reporting frameworks for transcriptomics data offers improved transparency and reproducibility of research and an opportunity to identify barriers to adoption of these NAMs, especially in environmental toxicology and ecotoxicology with aquatic models. Improved reporting also allows for reexamination of existing data, limiting needs for experiment replication and further reducing animal experimentation. Here, we use a standardized form of data reporting for omics-based studies, the Organisation for Economic Co-operation and Development omics reporting framework, which specifically reports on a list of parameters that should be included in transcriptomics studies used in a regulatory context. We focused specifically on fish studies using RNA- Sequencing (Seq)/microarray technologies within a toxicology context. Inconsistencies in reporting and methodologies among the experimental designs (toxicology vs. molecular characterization) were observed in addition to foundational differences in reporting of sample concentration or preparation or quality assessments, which can affect reproducibility and read across, confidence in results, and contribute substantially to understanding molecular mechanisms of toxicants and toxins. Our findings present an opportunity for improved research reporting. We also provide several recommendations as logical steps to reduce barriers to adoption of transcriptomics within environmental toxicology and ecotoxicology.

Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

Nanopore long-read sequencing is an emerging approach for studying genomes, including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We find that telomeres in many organisms are frequently miscalled. We demonstrate that tuning of nanopore basecalling models leads to improved recovery and analysis of telomeric regions, with minimal negative impact on other genomic regions. We highlight the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions, and showcase how artefacts can be resolved by improvements in nanopore basecalling models.