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Orehova M, Plavec J, Kocman V. High-Resolution Structure of RNA G-Quadruplex Containing Unique Structural Motifs Originating from the 5'-UTR of Human Tyrosine Kinase 2 (TYK2). ACS OMEGA 2024; 9:7215-7229. [PMID: 38371751 PMCID: PMC10870306 DOI: 10.1021/acsomega.3c09592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Tyrosine kinase 2 (TYK2) is a member of the JAK family of nonreceptor-associated tyrosine kinases together with highly homologous JAK1, JAK2, and JAK3 paralogues. Overexpression of TYK2 is associated with several inflammatory diseases, including severe complications during the COVID-19 infection. Since the downregulation of JAK paralogues could lead to serious health consequences or even death, it is critical to avoid it when designing drugs to suppress TYK2. To achieve the required specificity only for TYK2, researchers have recently selectively targeted TYK2 mRNA by developing antisense oligonucleotides. In this work, we expand the target space of TYK2 mRNA by showing that the mRNA adopts tetra-helical noncanonical structures called G-quadruplexes. We identified a TYKwt RNA oligonucleotide from the 5'-UTR of TYK2 mRNA, which adopts multiple different parallel G-quadruplexes that exist at equilibrium. Using NMR spectroscopy, we showed that some of the G-quadruplexes adopt unique structural motifs, mainly due to the formation of a stable GA bulge. Using guanine to uridine substitutions, we prepared the oligonucleotide TYK3_U6, which serves as an excellent model for the bulged G-quadruplexes formed by the TYKwt oligonucleotide. NMR structural analysis, including data on the residual coupling constants (RDC) of the loop regions, unveiled that the studied three-quartet parallel G-quadruplex contains many unusual structural features such as a G(U)A bulge, a guanine residue in the syn conformation, A and U residues stacked on the top G-quartet, and a well-defined adenine from a three-residue long propeller loop oriented in the groove, all of which could be valuable targets for future drug design.
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Affiliation(s)
- Maria Orehova
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, 1000 Ljubljana, Slovenia
| | - Vojč Kocman
- Slovenian
NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- EN-FIST
Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
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Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W. Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription. PLANT PHYSIOLOGY 2022; 188:1632-1648. [PMID: 34893906 PMCID: PMC8896617 DOI: 10.1093/plphys/kiab566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 06/01/2023]
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Francesco Rota Sperti
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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3
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Zacheja T, Toth A, Harami GM, Yang Q, Schwindt E, Kovács M, Paeschke K, Burkovics P. Mgs1 protein supports genome stability via recognition of G-quadruplex DNA structures. FASEB J 2020; 34:12646-12662. [PMID: 32748509 DOI: 10.1096/fj.202000886r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/19/2020] [Accepted: 07/10/2020] [Indexed: 01/02/2023]
Abstract
The integrity of the genetic material is crucial for every organism. One intrinsic attack to genome stability is stalling of the replication fork which can result in DNA breakage. Several factors, such as DNA lesions or the formation of stable secondary structures (eg, G-quadruplexes) can lead to replication fork stalling. G-quadruplexes (G4s) are well-characterized stable secondary DNA structures that can form within specific single-stranded DNA sequence motifs and have been shown to block/pause the replication machinery. In most genomes several helicases have been described to regulate G4 unfolding to preserve genome integrity, however, different experiments raise the hypothesis that processing of G4s during DNA replication is more complex and requires additional, so far unknown, proteins. Here, we show that the Saccharomyces cerevisiae Mgs1 protein robustly binds to G4 structures in vitro and preferentially acts at regions with a strong potential to form G4 structures in vivo. Our results suggest that Mgs1 binds to G4-forming sites and has a role in the maintenance of genome integrity.
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Affiliation(s)
- Theresa Zacheja
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Agnes Toth
- Biological Research Centre, Institute of Genetics, Szeged, Hungary.,Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gabor M Harami
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Qianlu Yang
- Department of Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Eike Schwindt
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Mihály Kovács
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany.,Department of Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Burkovics
- Biological Research Centre, Institute of Genetics, Szeged, Hungary
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De Fenza M, Eremeeva E, Troisi R, Yang H, Esposito A, Sica F, Herdewijn P, D'Alonzo D, Guaragna A. Structure-Activity Relationship Study of a Potent α-Thrombin Binding Aptamer Incorporating Hexitol Nucleotides. Chemistry 2020; 26:9589-9597. [PMID: 32363791 DOI: 10.1002/chem.202001504] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/29/2020] [Indexed: 12/13/2022]
Abstract
The replacement of one or more nucleotide residues in the potent α-thrombin-binding aptamer NU172 with hexitol-based nucleotides has been devised to study the effect of these substitutions on the physicochemical and functional properties of the anticoagulant agent. The incorporation of single hexitol nucleotides at the T9 and G18 positions of NU172 substantially retained the physicochemical features of the parent oligonucleotide, as a result of the biomimetic properties of the hexitol backbone. Importantly, the NU172-TH 9 mutant exhibited a higher binding affinity toward human α-thrombin than the native aptamer and an improved stability even after 24 h in 90 % human serum, with a significant increase in the estimated half-life. The anticoagulant activity of the modified oligonucleotide was also found to be slightly preferable to NU172. Overall, these results confirm the potential of hexitol nucleotides as biomimetic agents, while laying the foundations for the development of NU172-inspired α-thrombin-binding aptamers.
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Affiliation(s)
- Maria De Fenza
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Elena Eremeeva
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Romualdo Troisi
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Hui Yang
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Anna Esposito
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Filomena Sica
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Piet Herdewijn
- Rega Institute for Medical Research, Herestraat 49-box 1041, 3000, Leuven, Belgium
| | - Daniele D'Alonzo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Annalisa Guaragna
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
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