Novel eye genes systematically discovered through an integrated analysis of mouse transcriptomes and phenome

Chiang, Chia-Yin; Ching, Yung-Hao; Chang, Ting-Yan; Hu, Liang-Shuan; Yong, Yee Siang; Keak, Pei Ying; Mustika, Ivana; Lin, Ming-Der; Liao, Ben-Yang

doi:10.1016/j.csbj.2019.12.009

Cited by 10 publications

(7 citation statements)

References 72 publications

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“…The paralog regions overlapped the genes signal peptidase complex subunit 3 ( spcs3 ), WD repeat domain 17 ( wdr17 ), and ankyrin repeat and SOCS box containing 5 ( asb5 ). Their functions in fish are not well characterized; however, Wdr17 has a function in eyes in mice (Chiang et al., 2020), and there is evidence that spectral sensitivity and eye pigments differ in freshwater and seawater life stages in salmon (Temple et al., 2008). spcs3 and asb5 have been assigned to Reactome pathways (https://reactome.org) such as “Viral mRNA Translation,” and “Class I MHC mediated antigen processing and presentation”, respectively, suggesting that these might be related to resistance against seaborne diseases.…”

Section: Resultsmentioning

confidence: 99%

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Kjærner-Semb

Edvardsen

Ayllón

et al. 2020

Evolutionary Applications

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Section: Resultsmentioning

confidence: 99%

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Kjærner-Semb

Edvardsen

Ayllón

et al. 2020

Evolutionary Applications

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“…p2ry2.1-TBM 5 -TCGTGATCCAGATATAGATACTTTC-3 (this study); p2ry2.2-TBM 5 -GTTGTTAAATGCTGCCATCCTGATG-3 (this study); p2ry2.3-TBM 5 -TCATTCATTTTCCTTCACTTAGTCT-3 (this study); ada-TBM 5 -TCCATTCATTTCAGCCATTGTGTTG-3 (this study); ada-SBM 5 -AACAACAGGACACCACTAACCTTAG-3 (this study); ada2a-TBM 5 -TGCATGTCTGTAAGGTAATTCAACC-3 (this study); ada2b-TBM 5 -GCTTATGCTACTCATTGCTCCCAGC-3 [43]; adal-TBM 5 -AAAGAGATCCGCTTCGGTGTCCATC-3 [44]; adora1a-SBM 5 -ATTAAAATCTTATTACCTCATTGGT-3 (this study); adora1b-TBM 5 -GAGAGATCCTCGGGCATTCTTGCAC-3 [45]; adora2b-TBM 5 -CAATGGCGATGTAGAGCGAATCCAT-3 [46]; adora2aa-SBM 5 -AGAAACACCCTTCACTCACCTAAGC-3 [47]; adora2ab-TBM 5 -GTGCTATCAACCAGTGTGAAAGGAT-3 [48]; p53-MO 5 -GCGCCATTGCTTTGCAAGAATTG-3 [49]; Standard control (ctrl) MO 5 -CCTCTTACCTCAGTTACAATTTATA-3'. All MOs were co-injected with p53-MO to reduce unspecific effects [49].…”

Section: Morpholino Oligonucleotides (Mos) Gene Targetingmentioning

confidence: 69%

Control of Directed Cell Migration after Tubular Cell Injury by Nucleotide Signaling

Gessler

Guthmann

Schuler

et al. 2022

IJMS

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Acute kidney injury (AKI) is a common complication of severe human diseases, resulting in increased morbidity and mortality as well as unfavorable long-term outcomes. Although the mammalian kidney is endowed with an amazing capacity to recover from AKI, little progress has been made in recent decades to facilitate recovery from AKI. To elucidate the early repair mechanisms after AKI, we employed the zebrafish pronephros injury model. Since damaged cells release large amounts of ATP and ATP-degradation products to signal apoptosis or necrosis to neighboring cells, we examined how depletion of purinergic and adenosine receptors impacts the directed cell migration that ensues immediately after a laser-induced tubular injury. We found that depletion of the zebrafish adenosine receptors adora1a, adora1b, adora2aa, and adora2ab significantly affected the repair process. Similar results were obtained after depletion of the purinergic p2ry2 receptor, which is highly expressed during zebrafish pronephros development. Released ATP is finally metabolized to inosine by adenosine deaminase. Depletion of zebrafish adenosine deaminases ada and ada2b interfered with the repair process; furthermore, combinations of ada and ada2b, or ada2a and ada2b displayed synergistic effects at low concentrations, supporting the involvement of inosine signaling in the repair process after a tubular injury. Our findings suggest that nucleotide-dependent signaling controls immediate migratory responses after tubular injury.

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“…It can induce genotoxic stress and DNA damage ( Andrysik et al, 2010 ), which is one of the underlying mechanisms of AMD. Additionally, PLK5 is specifically expressed in the eye ( de Cárcer et al, 2011 ) and is a candidate gene modulating the proper development and function of mice eyes ( Chiang et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Predicting late-stage age-related macular degeneration by integrating marginally weak SNPs in GWA studies

Zhou

Zhang²,

Ding³

et al. 2023

Front. Genet.

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Introduction: Age-related macular degeneration (AMD) is a progressive neurodegenerative disease and the leading cause of blindness in developed countries. Current genome-wide association studies (GWAS) for late-stage age-related macular degeneration are mainly single-marker-based approaches, which investigate one Single-Nucleotide Polymorphism (SNP) at a time and postpone the integration of inter-marker Linkage-disequilibrium (LD) information in the downstream fine mappings. Recent studies showed that directly incorporating inter-marker connection/correlation into variants detection can help discover novel marginally weak single-nucleotide polymorphisms, which are often missed in conventional genome-wide association studies, and can also help improve disease prediction accuracy.Methods: Single-marker analysis is performed first to detect marginally strong single-nucleotide polymorphisms. Then the whole-genome linkage-disequilibrium spectrum is explored and used to search for high-linkage-disequilibrium connected single-nucleotide polymorphism clusters for each strong single-nucleotide polymorphism detected. Marginally weak single-nucleotide polymorphisms are selected via a joint linear discriminant model with the detected single-nucleotide polymorphism clusters. Prediction is made based on the selected strong and weak single-nucleotide polymorphisms.Results: Several previously identified late-stage age-related macular degeneration susceptibility genes, for example, BTBD16, C3, CFH, CFHR3, HTARA1, are confirmed. Novel genes DENND1B, PLK5, ARHGAP45, and BAG6 are discovered as marginally weak signals. Overall prediction accuracy of 76.8% and 73.2% was achieved with and without the inclusion of the identified marginally weak signals, respectively.Conclusion: Marginally weak single-nucleotide polymorphisms, detected from integrating inter-marker linkage-disequilibrium information, may have strong predictive effects on age-related macular degeneration. Detecting and integrating such marginally weak signals can help with a better understanding of the underlying disease-development mechanisms for age-related macular degeneration and more accurate prognostics.

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Novel eye genes systematically discovered through an integrated analysis of mouse transcriptomes and phenome

Cited by 10 publications

References 72 publications

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere

Control of Directed Cell Migration after Tubular Cell Injury by Nucleotide Signaling

Predicting late-stage age-related macular degeneration by integrating marginally weak SNPs in GWA studies

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