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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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Xu X, Liu R, Li Y, Zhang C, Guo C, Zhu J, Dong J, Ouyang L, Momeni MR. Spinal Cord Injury: From MicroRNAs to Exosomal MicroRNAs. Mol Neurobiol 2024:10.1007/s12035-024-03954-7. [PMID: 38261255 DOI: 10.1007/s12035-024-03954-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
Spinal cord injury (SCI) is an unfortunate experience that may generate extensive sensory and motor disabilities due to the destruction and passing of nerve cells. MicroRNAs are small RNA molecules that do not code for proteins but instead serve to regulate protein synthesis by targeting messenger RNA's expression. After SCI, secondary damage like apoptosis, oxidative stress, inflammation, and autophagy occurs, and differentially expressed microRNAs show a function in these procedures. Almost all animal and plant cells release exosomes, which are sophisticated formations of lipid membranes. These exosomes have the capacity to deliver significant materials, such as proteins, RNAs and lipids, to cells in need, regulating their functions and serving as a way of communication. This new method offers a fresh approach to treating spinal cord injury. Obviously, the exosome has the benefit of conveying the transported material across performing regulatory activities and the blood-brain barrier. Among the exosome cargoes, microRNAs, which modulate their mRNA targets, show considerable promise in the pathogenic diagnosis, process, and therapy of SCI. Herein, we describe the roles of microRNAs in SCI. Furthermore, we emphasize the importance of exosomal microRNAs in this disease.
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Affiliation(s)
- Xiangyang Xu
- Spinal Surgery, Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan, 450003, China
| | - Ruyin Liu
- Spinal Surgery, Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan, 450003, China
| | - Yunpeng Li
- Spinal Surgery, Henan Province Hospital of Traditional Chinese Medicine, The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Zhengzhou, Henan, 450003, China
| | - Cheng Zhang
- College of Traditional Chinese Medicine Orthopedics and Traumatology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, 450003, China
| | - Chuanghao Guo
- College of Traditional Chinese Medicine Orthopedics and Traumatology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, 450003, China
| | - Jiong Zhu
- College of Traditional Chinese Medicine Orthopedics and Traumatology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, 450003, China
| | - Jiaan Dong
- College of Traditional Chinese Medicine Orthopedics and Traumatology, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, 450003, China
| | - Liyun Ouyang
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, 11700, Malaysia.
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