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Bertram H, Wilhelmi S, Rajavel A, Boelhauve M, Wittmann M, Ramzan F, Schmitt AO, Gültas M. Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks. BIOLOGY 2023; 12:969. [PMID: 37508399 PMCID: PMC10375970 DOI: 10.3390/biology12070969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.
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Affiliation(s)
- Hendrik Bertram
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Selina Wilhelmi
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Marc Boelhauve
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Margareta Wittmann
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
| | - Faisal Ramzan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany; (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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Mai TL, Chuang TJ. A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations. Genome Res 2019; 29:1766-1776. [PMID: 31515285 PMCID: PMC6836733 DOI: 10.1101/gr.246033.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated with the deleteriousness of A-to-G genomic changes and positively correlated with that of G-to-A genomic changes within the population. We find a significantly negative correlation between nonsynonymous editing activities and allele frequency of A within the population. This negative editing-allele frequency correlation is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G-to-A changes increases with increasing deleterious effects of the changes. Moreover, the deleteriousness of G-to-A changes is significantly positively correlated with the percentage of editing enzyme binding motifs at the variants. Overall, we show that nonsynonymous editing is associated with the increased burden of G-to-A missense mutations in healthy individuals, expanding RNA editing in pathogenomics studies.
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Affiliation(s)
- Te-Lun Mai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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Hung LY, Chen YJ, Mai TL, Chen CY, Yang MY, Chiang TW, Wang YD, Chuang TJ. An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species. Genome Biol Evol 2018; 10:521-537. [PMID: 29294013 PMCID: PMC5800060 DOI: 10.1093/gbe/evx277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 12/12/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization.
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Affiliation(s)
- Li-Yuan Hung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yen-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Te-Lun Mai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Min-Yu Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tai-Wei Chiang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Da Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Trees-Juen Chuang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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Rozman V, Kunej T. Harnessing Omics Big Data in Nine Vertebrate Species by Genome-Wide Prioritization of Sequence Variants with the Highest Predicted Deleterious Effect on Protein Function. ACTA ACUST UNITED AC 2018; 22:410-421. [DOI: 10.1089/omi.2018.0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Vita Rozman
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
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