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Ouyang Z, Liu F, Li W, Wang J, Chen B, Zheng Y, Li Y, Tao H, Xu X, Li C, Cong Y, Li H, Bo X, Chen H. The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model. Nucleic Acids Res 2024:gkae441. [PMID: 38813828 DOI: 10.1093/nar/gkae441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.
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Affiliation(s)
- Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Feng Liu
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, China
| | - Wanying Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Junting Wang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yang Zheng
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Huan Tao
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuwen Cong
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
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Mori G, Liuzzi A, Ronda L, Di Palma M, Chegkazi MS, Bui S, Garcia-Maya M, Ragazzini J, Malatesta M, Della Monica E, Rivetti C, Antin PB, Bettati S, Steiner RA, Percudani R. Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism. Mol Biol Evol 2023; 40:msad200. [PMID: 37695804 PMCID: PMC10517255 DOI: 10.1093/molbev/msad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/13/2023] Open
Abstract
Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that the Gallus gallus gene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property that we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with the transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.
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Affiliation(s)
- Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Anastasia Liuzzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Michele Di Palma
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Magda S Chegkazi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Mitla Garcia-Maya
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Jasmine Ragazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Emanuele Della Monica
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Parker B Antin
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, USA
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberto A Steiner
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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Karpowicz SJ. Kinetics of taurine biosynthesis metabolites with reactive oxygen species: Implications for antioxidant-based production of taurine. Biochim Biophys Acta Gen Subj 2022; 1866:130131. [DOI: 10.1016/j.bbagen.2022.130131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/16/2022] [Accepted: 03/13/2022] [Indexed: 11/27/2022]
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