Academic Bibliography

 Search 200 years of publications by Ghent University researchers.
Advanced search
1 file | 2.86 MB
Add to list
  1. Search results
  2. A proteogenomic atlas of the human ne...

A proteogenomic atlas of the human neural retina

Tabea V. Riepe, Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey, Suzanne E. de Bruijn, Erica Boonen, Tomasz Z. Tomkiewicz, Michael Kwint, Jolein Gloerich, Hans J. C. T. Wessels, et al.
(2024) FRONTIERS IN GENETICS. 15.
Author
Organization
Project
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.
Keywords
MUTATIONS, GENE, IDENTIFICATION, LENGTH, BBS8, neural retina, isoform, alternative splicing, multi-omics, long-read sequencing, proteogenomics, mass spectrometry, inherited retinal disease (IRD)

Downloads

  • Download
    A proteogenomic atlas of the human neural retina.pdf
    • full text (Published version)
    • |
    • open access
    • |
    • PDF
    • |
    • 2.86 MB

Citation

Please use this url to cite or link to this publication:

MLA
Riepe, Tabea V., et al. “A Proteogenomic Atlas of the Human Neural Retina.” FRONTIERS IN GENETICS, vol. 15, 2024, doi:10.3389/fgene.2024.1451024.
APA
Riepe, T. V., Stemerdink, M., Salz, R., Dueñas Rey, A., de Bruijn, S. E., Boonen, E., … ’t Hoen, P. A. C. (2024). A proteogenomic atlas of the human neural retina. FRONTIERS IN GENETICS, 15. https://doi.org/10.3389/fgene.2024.1451024
Chicago author-date
Riepe, Tabea V., Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey, Suzanne E. de Bruijn, Erica Boonen, Tomasz Z. Tomkiewicz, et al. 2024. “A Proteogenomic Atlas of the Human Neural Retina.” FRONTIERS IN GENETICS 15. https://doi.org/10.3389/fgene.2024.1451024.
Chicago author-date (all authors)
Riepe, Tabea V., Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey, Suzanne E. de Bruijn, Erica Boonen, Tomasz Z. Tomkiewicz, Michael Kwint, Jolein Gloerich, Hans J. C. T. Wessels, Emma Delanote, Elfride De Baere, Filip Van Nieuwerburgh, Sarah De Keulenaer, Barbara Ferrari, Stefano Ferrari, Frauke Coppieters, Frans P. M. Cremers, Erwin van Wyk, Susanne Roosing, Erik de Vrieze, and Peter A. C. ’t Hoen. 2024. “A Proteogenomic Atlas of the Human Neural Retina.” FRONTIERS IN GENETICS 15. doi:10.3389/fgene.2024.1451024.
Vancouver
1.
Riepe TV, Stemerdink M, Salz R, Dueñas Rey A, de Bruijn SE, Boonen E, et al. A proteogenomic atlas of the human neural retina. FRONTIERS IN GENETICS. 2024;15.
IEEE
[1]
T. V. Riepe et al., “A proteogenomic atlas of the human neural retina,” FRONTIERS IN GENETICS, vol. 15, 2024.
@article{01JC5XWM7RVBTGZTZ4QHK9AQBX,
  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.}},
  articleno    = {{1451024}},
  author       = {{Riepe, Tabea V. and Stemerdink, Merel and Salz, Renee and Dueñas Rey, Alfredo and de Bruijn, Suzanne E. and Boonen, Erica and Tomkiewicz, Tomasz Z. and Kwint, Michael and Gloerich, Jolein and Wessels, Hans J. C. T. and Delanote, Emma and De Baere, Elfride and Van Nieuwerburgh, Filip and De Keulenaer, Sarah and Ferrari, Barbara and Ferrari, Stefano and Coppieters, Frauke and Cremers, Frans P. M. and van Wyk, Erwin and Roosing, Susanne and de Vrieze, Erik and 't Hoen, Peter A. C.}},
  issn         = {{1664-8021}},
  journal      = {{FRONTIERS IN GENETICS}},
  keywords     = {{MUTATIONS,GENE,IDENTIFICATION,LENGTH,BBS8,neural retina,isoform,alternative splicing,multi-omics,long-read sequencing,proteogenomics,mass spectrometry,inherited retinal disease (IRD)}},
  language     = {{eng}},
  pages        = {{17}},
  title        = {{A proteogenomic atlas of the human neural retina}},
  url          = {{http://doi.org/10.3389/fgene.2024.1451024}},
  volume       = {{15}},
  year         = {{2024}},
}
Altmetric
View in Altmetric
Web of Science
Times cited: