CLN3 transcript complexity revealed by long-read RNA sequencing analysis.

BMC Med Genomics

Great Ormond Street Institute of Child Health, University College London, London, WC1E 1EH, UK.

Published: October 2024

AI Article Synopsis

  • Batten disease, particularly juvenile CLN3 disease, involves rare neurodegenerative disorders linked to a common "1-kb" deletion in the CLN3 gene, necessitating deeper research into CLN3 transcripts in healthy samples.
  • Using PacBio long-read RNA sequencing from control tissues, researchers discovered over 100 novel CLN3 transcripts and highlighted the complexity of their expression, with no single dominant form identified.
  • These findings emphasize the need to examine both typical and atypical CLN3 protein isoforms, revealing that various transcripts may impact disease mechanisms and potential treatment strategies.

Article Abstract

Background: Batten disease is a group of rare inherited neurodegenerative diseases. Juvenile CLN3 disease is the most prevalent type, and the most common pathogenic variant shared by most patients is the "1-kb" deletion which removes two internal coding exons (7 and 8) in CLN3. Previously, we identified two transcripts in patient fibroblasts homozygous for the 1-kb deletion: the 'major' and 'minor' transcripts. To understand the full variety of disease transcripts and their role in disease pathogenesis, it is necessary to first investigate CLN3 transcription in "healthy" samples without juvenile CLN3 disease.

Methods: We leveraged PacBio long-read RNA sequencing datasets from ENCODE to investigate the full range of CLN3 transcripts across various tissues and cell types in human control samples. Then we sought to validate their existence using data from different sources.

Results: We found that a readthrough gene affects the quantification and annotation of CLN3. After taking this into account, we detected over 100 novel CLN3 transcripts, with no dominantly expressed CLN3 transcript. The most abundant transcript has median usage of 42.9%. Surprisingly, the known disease-associated 'major' transcripts are detected. Together, they have median usage of 1.5% across 22 samples. Furthermore, we identified 48 CLN3 ORFs, of which 26 are novel. The predominant ORF that encodes the canonical CLN3 protein isoform has median usage of 66.7%, meaning around one-third of CLN3 transcripts encode protein isoforms with different stretches of amino acids. The same ORFs could be found with alternative UTRs. Moreover, we were able to validate the translational potential of certain transcripts using public mass spectrometry data.

Conclusion: Overall, these findings provide valuable insights into the complexity of CLN3 transcription, highlighting the importance of studying both canonical and non-canonical CLN3 protein isoforms as well as the regulatory role of UTRs to fully comprehend the regulation and function(s) of CLN3. This knowledge is essential for investigating the impact of the 1-kb deletion and rare pathogenic variants on CLN3 transcription and disease pathogenesis.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11451007PMC
http://dx.doi.org/10.1186/s12920-024-02017-zDOI Listing

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