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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

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

Hao-Yu Zhang¹, Christopher Minnis¹, Emil Gustavsson¹

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

BMC Medical Genomics

|October 4, 2024

Summary

This study reveals over 100 novel CLN3 transcripts and 48 CLN3 ORFs in healthy human samples, challenging previous understanding of CLN3 gene expression and Batten disease pathogenesis.

Keywords:

CLN3 Alternative splicing Batten disease Juvenile CLN3 disease Long-read RNA sequencing Neuronal ceroid lipofuscinoses Readthrough gene Transcription

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Last Updated: Jun 11, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

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Published on: July 2, 2010

Area of Science:

Genetics
Molecular Biology
Neuroscience

Background:

Batten disease is a rare inherited neurodegenerative disorder.
Juvenile CLN3 disease, the most common type, is often caused by a "1-kb" deletion in the CLN3 gene.
Understanding CLN3 transcription in healthy individuals is crucial before studying disease-specific variants.

Purpose of the Study:

To investigate the full spectrum of CLN3 transcripts in healthy human samples.
To characterize CLN3 transcription and identify novel transcripts and open reading frames (ORFs).
To establish a baseline for understanding CLN3 gene expression in the context of Batten disease.

Main Methods:

Utilized PacBio long-read RNA sequencing data from ENCODE for comprehensive transcript analysis.
Analyzed human control samples across various tissues and cell types.
Validated transcript existence using diverse public datasets.

Main Results:

Identified over 100 novel CLN3 transcripts and 48 CLN3 ORFs (26 novel) after accounting for readthrough genes.
No single dominant CLN3 transcript was found; the most abundant had 42.9% median usage.
Canonical CLN3 protein isoform ORF usage was 66.7%, indicating significant alternative translation.
Disease-associated "major" transcripts were detected but had low median usage (1.5%).
Alternative UTRs were associated with identified ORFs, and translational potential was validated via mass spectrometry.

Conclusions:

CLN3 transcription is highly complex, involving numerous novel transcripts and ORFs.
Both canonical and non-canonical CLN3 protein isoforms, along with UTRs, are critical for understanding CLN3 function.
This foundational knowledge is vital for dissecting the impact of the "1-kb" deletion and other variants on CLN3 transcription and Batten disease pathogenesis.