A proteogenomic atlas of the human neural retina
Open accessPublished version of a preprint
Abstract
The human neural retina is a complex tissue with abundant alternative splicing and more than 10% of genetic variants linked to inherited retinal diseases (IRDs) alter splicing. Traditional short-read RNA-sequencing methods have been used for understanding retina-specific splicing but have limitations in detailing transcript isoforms. To address this, we generated a proteogenomic atlas that combines PacBio long-read RNA-sequencing data with mass spectrometry and whole genome sequencing data of three healthy human neural retina samples. We identified nearly 60,000 transcript isoforms, of which approximately one-third are novel. Additionally, ten novel peptides confirmed novel transcript isoforms. For instance, we identified a novel IMPDH1 isoform with a novel combination of known exons that is supported by peptide evidence. Our research underscores the potential of in-depth tissue-specific transcriptomic analysis to enhance our grasp of tissue-specific alternative splicing. The data underlying the proteogenomic atlas are available via EGA with identifier EGAD50000000101, via ProteomeXchange with identifier PXD045187, and accessible through the UCSC genome browser.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Proteoform: a single term describing protein complexity
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“Moreover, earlier studies primarily focused on transcript isoforms, but it is also important to investigate the in fl uence of transcriptome diversity on proteome diversity (Smith et al., 2013).”
BackgroundRatnapriya, R., Sosina, O. A., Starostik, M. R., Kwicklis, M., Kapphahn, R. J., Fritsche, L. G., Walton, A., Arvanitis, M., Gieser, L., Pietraszkiewicz, A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0351-9 · Cited by 312 · see citing works
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- Authors
- Riepe, T. V., Stemerdink, M., Salz, R., Rey, A. D., de Bruijn, S. E., Boonen, E., Tomkiewicz, T. Z., Kwint, M., Gloerich, J., Wessels, H. J. C. T., Delanote, E., De Baere, E., van Nieuwerburgh, F., De Keulenaer, S., Ferrari, B., Ferrari, S., Coppieters, F., Cremers, F. P. M., van Wyk, E., Roosing, S., de Vrieze, E., & ‘t Hoen, P. A. C.
- Affiliations
- Radboud University Nijmegen (NL)
- Radboud University Medical Center (NL)
- Ghent University Hospital (BE)
- Veneto Eye Bank Foundation (IT)
- ORCID
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2024-09-19
- Volume
- 15
- Pages
- 1451024-1451024
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC11450717
- OpenAlex
- W4402657164
- Cited by
- 5
- References
- 3
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 1
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion, cc-by)
- Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (184.034.019)
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Institute of Neurological Disorders and Stroke
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- proteogenomics, alternative splicing, mRNA isoforms, novel isoforms, novel peptides, IMPDH1, inherited retinal disease, long-read RNA sequencing
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