Vision-related convergent gene losses reveal SERPINE3’s unknown role in the eye
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Abstract
Despite decades of research, knowledge about the genes that are important for development and function of the mammalian eye and are involved in human eye disorders remains incomplete. During mammalian evolution, mammals that naturally exhibit poor vision or regressive eye phenotypes have independently lost many eye-related genes. This provides an opportunity to predict novel eye-related genes based on specific evolutionary gene loss signatures. Building on these observations, we performed a genome-wide screen across 49 mammals for functionally uncharacterized genes that are preferentially lost in species exhibiting lower visual acuity values. The screen uncovered several genes, including SERPINE3 , a putative serine proteinase inhibitor. A detailed investigation of 381 additional mammals revealed that SERPINE3 is independently lost in 18 lineages that typically do not primarily rely on vision, predicting a vision-related function for this gene. To test this, we show that SERPINE3 has the highest expression in eyes of zebrafish and mouse. In the zebrafish retina, serpine3 is expressed in Müller glia cells, a cell type essential for survival and maintenance of the retina. A CRISPR-mediated knockout of serpine3 in zebrafish resulted in alterations in eye shape and defects in retinal layering. Furthermore, two human polymorphisms that are in linkage with SERPINE3 are associated with eye-related traits. Together, these results suggest that SERPINE3 has a role in vertebrate eyes. More generally, by integrating comparative genomics with experiments in model organisms, we show that screens for specific phenotype-associated gene signatures can predict functions of uncharacterized genes.
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TOGA enables phylogenomic analyses as well as screens for selection patterns and gene losses that are linked to relevant phenotypes.
“First, by detecting inactivated genes and providing orthologous sequences for codon alignments, TOGA enables phylogenomic analyses as well as screens for selection patterns and gene losses that are linked to relevant phenotypes (6, 35–38).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [38]
The Materials and methods sections on investigating SERPINE3 losses and selection analysis say TOGA classifies potentially lost genes and supplies codon sequences used to test selection. The phenotype-linked gene-loss screen used a previously generated dataset and the Forward Genomics approach, rather than TOGA. Thus the paper supports TOGA’s role in gene-loss detection and selection analysis, but not the attributed role in that screen. (LLM, conf=0.83)
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Flagged first, then by citations
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Cited by
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Integrating gene annotation with orthology inference at scale
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Self-citation
- Authors
- Indrischek, H., Hammer, J., Machate, A., Hecker, N., Kirilenko, B., Roscito, J., Hans, S., Norden, C., Brand, M., & Hiller, M.
- Affiliations
- Goethe University Frankfurt (DE)
- Center for Regenerative Therapies Dresden (DE)
- Max Planck Institute for the Physics of Complex Systems (DE)
- Max Planck Institute of Molecular Cell Biology and Genetics (DE)
- Corresponding author
- Brand, Michael
- Hiller, Michael
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2022-06-21
- Volume
- 11
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC9355568
- OpenAlex
- W4283271507
- Cited by
- 21
- References
- 111
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 5 · 2023: 3 · 2022: 2
- FWCI
- 1.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lirias (KU Leuven) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Boehringer Ingelheim
- Max Planck Society
- Hessen State Ministry of Higher Education, Research and the Arts
- German Research Foundation (BR 1746/3 and BR 1746/6)
- European Research Council (Zf-BrainReg)
- Studienstiftung des Deutschen Volkes
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinal Development and Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Ocular Disorders and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- convergent evolution, gene loss, eye development, visual acuity, Müller cells, retina, serine protease inhibitors, zebrafish, mice, CRISPR knockout, human genetic polymorphism, eye shape, comparative genomics, mammalian evolution
- MeSH terms
- Animals, Blindness, Eye Proteins, Humans, Mammals, Retina, Vision, Ocular, Vision Disorders, Zebrafish, Genome, Zebrafish Proteins, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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