Targeted long-read RNA sequencing reveals the complexity of CLN3 transcription and the consequences of the most common 1-kb deletion in patients with juvenile CLN3 disease

Minnis, C. J.; Zhang, H.-Y.; Gustavsson, E.; Lee, J.; Anderson, C.; Gardner, E.; Schulz, A.; Nickel, M.; Arno, G.; Jurkute, N.; Webster, A. R.; Gammaldi, N.; Santorelli, F. M.; Gissen, P.; Mills, P.; Ryten, M.; Mole, S. E.

doi:10.1101/2025.04.24.650398

bioRxiv · 10.1101/2025.04.24.650398

Targeted long-read RNA sequencing reveals the complexity of CLN3 transcription and the consequences of the most common 1-kb deletion in patients with juvenile CLN3 disease

Minnis, C. J.·Zhang, H.-Y.·Gustavsson, E.·Lee, J.·Anderson, C.·Gardner, E.·Schulz, A.·Nickel, M.·Arno, G.·Jurkute, N.·Webster, A. R.·Gammaldi, N.·Santorelli, F. M.·Gissen, P.·Mills, P.·Ryten, M.·Mole, S. E.

View original source ↗Export metadata ↓

Abstract

Most genes are not yet fully annotated, and the extent of their transcript diversity and the roles and significance of specific isoforms is not understood. This information is therefore lacking for disease genes. The CLN3 gene underlies classic juvenile CLN3 disease, also known as juvenile neuronal ceroid lipofuscinosis, a rare paediatric neurodegenerative disorder. The most common cause of this biallelic disorder is a 1-kb intragenic deletion that removes two internal coding exons (exons 7 and 8). Here, we report findings from the first long-read RNA sequencing targeting CLN3 in blood samples derived from control individuals and from patients clinically and genetically diagnosed with juvenile CLN3 disease. We find that CLN3 transcription is complex, with >80 different transcripts encoding >35 different open reading frames (ORF) of different lengths, and no dominantly expressed transcript. The 1-kb deletion has direct consequences on this. This is consistent across patients, with total loss of some transcripts including those encoding the canonical 438 amino acid protein and other significant smaller isoforms. The highest expressed disease transcripts include those lacking exons 7 and 8 and encoding a 181 amino acid protein isoform, and other novel isoforms that lack additional exons and encode longer ORFs. The different effects on transcription of other CLN3 disease-causing variants are revealed in single patients. Together, these findings confirm the complexity of transcription at the CLN3 locus, reveal the impact of the 1-kb deletion and other variants on isoform abundance, and highlight the importance of understanding the contribution of these isoforms to CLN3 function in health and disease. Moreover, they impact the future design and development of personalised therapeutics and the design and generation of disease models. Finally, they underline the importance of full annotation for disease genes.

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Minnis, C. J., Zhang, H.-Y., Gustavsson, E., Lee, J., Anderson, C., Gardner, E., Schulz, A., Nickel, M., Arno, G., Jurkute, N., Webster, A. R., Gammaldi, N., Santorelli, F. M., Gissen, P., Mills, P., Ryten, M., Mole, S. E.. 2025-04-24. Targeted long-read RNA sequencing reveals the complexity of CLN3 transcription and the consequences of the most common 1-kb deletion in patients with juvenile CLN3 disease. https://doi.org/10.1101/2025.04.24.650398

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗

bioRxiv2026

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗

bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗