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Tao S, Run Y, Monchaud D, Zhang W. i-Motif DNA: identification, formation, and cellular functions. Trends Genet 2024:S0168-9525(24)00133-1. [PMID: 38902139 DOI: 10.1016/j.tig.2024.05.011] [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: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.
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Affiliation(s)
- Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yonghang Run
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6302, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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2
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Zhao P, Feng Y, Jiang P, Zhang W. Identification and functional characterization of i-motifs in plants. TRENDS IN PLANT SCIENCE 2024; 29:495-496. [PMID: 38402017 DOI: 10.1016/j.tplants.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/26/2024]
Affiliation(s)
- Pengtao Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Peng Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China.
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3
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Chen Y, Li J, Niu K, Peng Y, Song Q, Feng Q. G-quadruplex is involved in the regulation of BmSGF1 expression in the Silkworm, Bombyx mori. INSECT SCIENCE 2024. [PMID: 38439572 DOI: 10.1111/1744-7917.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 03/06/2024]
Abstract
Advanced DNA structures, such as the G-quadruplex (G4) and the i-motif, are widely but not randomly present in the genomes of many organisms. A G4 structure was identified in the promoter of the silk gland factor-1 gene (SGF1), which is the main regulatory gene for silk production in Bombyx mori. In this study, a BmSGF1 G4-/- homozygous mutant was generated with the G4 sequence knocked out. The promoter activity of BmSGF1 was lowered in the BmSGF1 G4-/- mutant. Pyridostatin (PDS) stabilized the G4 structure and increased the promoter activity of BmSGF1, whereas anti-sense oligonucleotide (ASO) complementary to the G4 sequence suppressed the promoter activity of BmSGF1. Compared with wild-type larvae, the deletion of the BmSGF1 G4 structure decreased both the expression of BmSGF1 and the fibroin heavy chain gene BmFib-H in the posterior silk gland and the weight of the cocoons. Overall, these results suggest that the promoter G4 structure of BmSGF1 participates in the transcription regulation of the BmSGF1 gene in the silkworm.
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Affiliation(s)
- Yanfei Chen
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qisheng Song
- Division of Plant Science & Technology, University of Missouri, Columbia, Missouri, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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4
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Lyu B, Song Q. The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands. eLife 2024; 12:RP91985. [PMID: 38391174 PMCID: PMC10942614 DOI: 10.7554/elife.91985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.
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Affiliation(s)
- Bo Lyu
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
| | - Qisheng Song
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
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5
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Feng Y, Ma X, Yang Y, Tao S, Ahmed A, Gong Z, Cheng X, Zhang W. The roles of DNA methylation on pH dependent i-motif (iM) formation in rice. Nucleic Acids Res 2024; 52:1243-1257. [PMID: 38180820 PMCID: PMC10853798 DOI: 10.1093/nar/gkad1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
I-motifs (iMs) are four-stranded non-B DNA structures containing C-rich DNA sequences. The formation of iMs is sensitive to pH conditions and DNA methylation, although the extent of which is still unknown in both humans and plants. To investigate this, we here conducted iMab antibody-based immunoprecipitation and sequencing (iM-IP-seq) along with bisulfite sequencing using CK (original genomic DNA without methylation-related treatments) and hypermethylated or demethylated DNA at both pH 5.5 and 7.0 in rice, establishing a link between pH, DNA methylation and iM formation on a genome-wide scale. We found that iMs folded at pH 7.0 displayed higher methylation levels than those formed at pH 5.5. DNA demethylation and hypermethylation differently influenced iM formation at pH 7.0 and 5.5. Importantly, CG hypo-DMRs (differentially methylated regions) and CHH (H = A, C and T) hyper-DMRs alone or coordinated with CG/CHG hyper-DMRs may play determinant roles in the regulation of pH dependent iM formation. Thus, our study shows that the nature of DNA sequences alone or combined with their methylation status plays critical roles in determining pH-dependent formation of iMs. It therefore deepens the understanding of the pH and methylation dependent modulation of iM formation, which has important biological implications and practical applications.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xing Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Asgar Ahmed
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur 5200, Bangladesh
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Xuejiao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
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6
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Ghezzo M, Grigoletto L, Rigo R, Herdewijn P, Groaz E, Sissi C. Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications. Biochimie 2023; 214:112-122. [PMID: 37558081 DOI: 10.1016/j.biochi.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2'-deoxyribose, arabinose, and 2'-deoxy-2'-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications. An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3'-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.
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Affiliation(s)
- Michele Ghezzo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Luca Grigoletto
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Riccardo Rigo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium
| | - Elisabetta Groaz
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy; KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
| | - Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5 35131, Padova, Italy.
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Pandey A, Roy S, Srivatsan SG. Probing the Competition between Duplex, G-Quadruplex and i-Motif Structures of the Oncogenic c-Myc DNA Promoter Region. Chem Asian J 2023; 18:e202300510. [PMID: 37541298 DOI: 10.1002/asia.202300510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/09/2023] [Indexed: 08/06/2023]
Abstract
Development of probe systems that provide unique spectral signatures for duplex, G-quadruplex (GQ) and i-motif (iM) structures is very important to understand the relative propensity of a G-rich-C-rich promoter region to form these structures. Here, we devise a platform using a combination of two environment-sensitive nucleoside analogs namely, 5-fluorobenzofuran-modified 2'-deoxyuridine (FBF-dU) and 5-fluoro-2'-deoxyuridine (F-dU) to study the structures adopted by a promoter region of the c-Myc oncogene. FBF-dU serves as a dual-purpose probe containing a fluorescent and 19 F NMR label. When incorporated into the C-rich sequence, it reports the formation of different iMs via changes in its fluorescence properties and 19 F signal. F-dU incorporated into the G-rich ON reports the formation of a GQ structure whose 19 F signal is clearly different from the signals obtained for iMs. Rewardingly, the labeled ONs when mixed with respective complementary strands allows us to determine the relative population of different structures formed by the c-Myc promoter by the virtue of the probe's ability to produce distinct and resolved 19 F signatures for different structures. Our results indicate that at physiological pH and temperature the c-Myc promoter forms duplex, random coil and GQ structures, and does not form an iM. Whereas at acidic pH, the mixture largely forms iM and GQ structures. Taken together, our system will complement existing tools and provide unprecedented insights on the population equilibrium and dynamics of nucleic acid structures under different conditions.
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Affiliation(s)
- Akanksha Pandey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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8
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Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
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9
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Deng Z, Zhang Y, Gao C, Shen W, Wang S, Ni X, Liu S, Li X. A transposon-introduced G-quadruplex motif is selectively retained and constrained to downregulate CYP321A1. INSECT SCIENCE 2022; 29:1629-1642. [PMID: 35226400 DOI: 10.1111/1744-7917.13021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Insects utilize xenobiotic compounds to up- and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G-quadruplexes (G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes. Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored. Here, we show that CYP321A1, a xenobiotic-metabolizing P450 from Helicoverpa zea, a polyphagous insect of economic importance, has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region. The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K+ . The G4 ligand N-methylmesoporphyrin IX (NMM) strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2. The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.
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Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wei Shen
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Shan Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinzhi Ni
- USDA-ARS, Crop Genetics and Breeding Research Unit, University of Georgia, Tifton Campus, Tifton, GA, USA
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
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Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures. J Biol Chem 2022; 298:102670. [PMID: 36334628 PMCID: PMC9709238 DOI: 10.1016/j.jbc.2022.102670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/27/2022] Open
Abstract
I-motifs are four-strand noncanonical secondary structures formed by cytosine (C)-rich sequences in living cells. The structural dynamics of i-motifs play essential roles in many cellular processes, such as telomerase inhibition, DNA replication, and transcriptional regulation. In cells, the structural dynamics of the i-motif can be modulated by the interaction of poly(C)-binding proteins (PCBPs), and the interaction is closely related to human health, through modulating the transcription of oncogenes and telomere stability. Therefore, the mechanisms of how PCBPs interact with i-motif structures are fundamentally important. However, the underlying mechanisms remain elusive. I-motif structures in the promoter of the c-MYC oncogene can be unfolded by heterogeneous nuclear ribonucleoprotein K (hnRNP K), a PCBP, to activate its transcription. Here, we selected this system as an example to comprehensively study the unfolding mechanisms. We found that the promoter sequence containing 5 C-runs preferred folding into type-1245 to type-1234 i-motif structures based on their folding stability, which was further confirmed by single-molecule FRET. In addition, we first revealed that the c-MYC i-motif structure was discretely resolved by hnRNP K through two intermediate states, which were assigned to the opposite hairpin and neighboring hairpin, as further confirmed by site mutations. Furthermore, we found all three KH (hnRNP K homology) domains of hnRNP K could unfold the c-MYC i-motif structure, and KH2 and KH3 were more active than KH1. In conclusion, this study may deepen our understanding of the interactions between i-motifs and PCBPs and may be helpful for drug development.
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11
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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12
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Li M, Tian R, Monchaud D, Zhang W. Omics studies of DNA G-/C-quadruplexes in plants. Trends Genet 2022; 38:999-1002. [PMID: 35853768 DOI: 10.1016/j.tig.2022.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
Genome-wide studies of DNA G- and C-quadruplexes (G4s and i-motifs, respectively) can boost the pace of progress towards a comprehensive understanding of their biological implications and practical applications in plants. We summarize the current state of knowledge about omics studies in order to highlight the current challenges and propose future directions to take studies of plant quadruplexes to the next step.
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Affiliation(s)
- Mengqi Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Ruiping Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China.
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13
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Khatik SY, Srivatsan SG. Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs. Bioconjug Chem 2022; 33:1515-1526. [PMID: 35819865 DOI: 10.1021/acs.bioconjchem.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although evidence for the existence and biological role of i-motif (iM) DNA structures in cells is emerging, probing their structural polymorphism and identifying physiologically active conformations using currently available tools remain a major challenge. Here, we describe the development of an innovative device to investigate the conformation equilibrium of different iMs formed by C-rich telomeric repeat and oncogenic B-raf promoter sequences using a new conformation-sensitive dual-purpose nucleoside probe. The nucleoside is composed of a trifluoromethyl-benzofuran-2-yl moiety at the C5 position of 2'-deoxyuridine, which functions as a responsive fluorescent and 19F NMR probe. While the fluorescent component is useful in monitoring and estimating the folding process, the 19F label provides spectral signatures for various iMs, thereby enabling a systematic analysis of their complex population equilibrium under different conditions (e.g., pH, temperature, metal ions, and cell lysate). Distinct 19F signals exhibited by the iMs formed by the human telomeric repeat helped in calculating their relative population. A battery of fluorescence and 19F NMR studies using native and mutated B-raf oligonucleotides gave valuable insights into the iM structure landscape and its dependence on environmental conditions and also helped in predicting the structure of the major iM conformation. Overall, our findings indicate that the probe is highly suitable for studying complex nucleic acid systems.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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14
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Xiang L, Niu K, Peng Y, Zhang X, Li X, Ye R, Yu G, Ye G, Xiang H, Song Q, Feng Q. DNA G-quadruplex structure participates in regulation of lipid metabolism through acyl-CoA binding protein. Nucleic Acids Res 2022; 50:6953-6967. [PMID: 35748856 PMCID: PMC9262599 DOI: 10.1093/nar/gkac527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022] Open
Abstract
G-quadruplex structure (G4) is a type of DNA secondary structure that widely exists in the genomes of many organisms. G4s are believed to participate in multiple biological processes. Acyl-CoA binding protein (ACBP), a ubiquitously expressed and highly conserved protein in eukaryotic cells, plays important roles in lipid metabolism by transporting and protecting acyl-CoA esters. Here, we report the functional identification of a G4 in the promoter of the ACBP gene in silkworm and human cancer cells. We found that G4 exists as a conserved element in the promoters of ACBP genes in invertebrates and vertebrates. The BmACBP G4 bound with G4-binding protein LARK regulated BmACBP transcription, which was blocked by the G4 stabilizer pyridostatin (PDS) and G4 antisense oligonucleotides. PDS treatment with fifth instar silkworm larvae decreased the BmACBP expression and triacylglycerides (TAG) level, resulting in reductions in fat body mass, body size and weight and growth and metamorphic rates. PDS treatment and knocking out of the HsACBP G4 in human hepatic adenocarcinoma HepG2 cells inhibited the expression of HsACBP and decreased the TAG level and cell proliferation. Altogether, our findings suggest that G4 of the ACBP genes is involved in regulation of lipid metabolism processes in invertebrates and vertebrates.
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Affiliation(s)
- Lijun Xiang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Kangkang Niu
- Correspondence may also be addressed to Kangkang Niu. Tel: +86 20 85215291; Fax: +86 20 85215291;
| | - Yuling Peng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoyu Li
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ruoqi Ye
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Guoxing Yu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Guojun Ye
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hui Xiang
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qisheng Song
- Division of Plant Sciences and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Qili Feng
- To whom correspondence should be addressed. Tel: +86 20 85215291; Fax: +86 20 85215291;
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15
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Chen Y, Niu K, Song Q, Feng Q. Effect of G-quadruplex loop mutations on the G-quadruplex formation, protein binding and transcription of BmPOUM2 in Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21876. [PMID: 35220618 DOI: 10.1002/arch.21876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
A G-quadruplex (G4) was identified in the promoter of transcription factor BmPOUM2 in Bombyx mori. This G4 structure contains three loops and is bound by transcription factor BmLARK, facilitating the transcription of BmPOUM2. However, the relationship between the structure and function of the BmPOUM2 G4 remains to be clarified. In this study, loop mutants of the BmPOUM2 G4 structure were generated to study the function of the structure in transcription regulation. The results revealed that mutations of Loops A and B could not completely suppress G4 formation, but affected the binding of the G4 structure with BmLARK and the promoter activity. The mutation (C-to-T) of the one-nucleotide-loop, Loop C, enhanced the G4 formation, its binding with BmLARK and the transcription activity of the BmPOUM2 promoter. It is speculated that the binding site of BmLARK probably is on the G-quartet planes, rather than on the loops, which may assist the maintenance and modification of the G4 structure and its protein binding activity.
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Affiliation(s)
- Yanfei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, Guangdong, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
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16
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Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif. Int J Mol Sci 2022; 23:ijms23073872. [PMID: 35409230 PMCID: PMC8998492 DOI: 10.3390/ijms23073872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.
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17
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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18
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Ma X, Feng Y, Yang Y, Li X, Shi Y, Tao S, Cheng X, Huang J, Wang XE, Chen C, Monchaud D, Zhang W. Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice. Nucleic Acids Res 2022; 50:3226-3238. [PMID: 35188565 PMCID: PMC8989525 DOI: 10.1093/nar/gkac121] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
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Affiliation(s)
- Xing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Ying Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xin Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Jian Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
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19
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Zhao Z, Li X, Cui Z, Tong T, Zhang Y, Zhang Y, Yang X, Keerthiga R, Fu C, Fu A. Synthesis of Hemiprotonic Phenanthroline-Phenanthroline + Compounds with both Antitumor and Antimicrobial Activity. J Med Chem 2022; 65:2532-2547. [PMID: 35073076 DOI: 10.1021/acs.jmedchem.1c01982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Currently, cancer patients with microbial infection are a severe challenge in clinical treatment. To address the problem, we synthesized hemiprotonic compounds based on the unique structure of hemiprotonic nucleotide base pairs in a DNA i-motif. These compounds were produced from phenanthroline (ph) dimerization with phenanthroline as a proton receptor and ammonium as a donor. The biological activity shows that the compounds have a selective antitumor effect through inducing cell apoptosis. The molecular mechanism could be related to specific inhibition of transcription factor PLAGL2 of tumor cells, assessed by transcriptomic analysis. Moreover, results show that the hemiprotonic ph-ph+ has broad-spectrum antibacterial and antifungal activities, and drug-resistant bacteria, including methicillin-resistant Staphylococcus aureus, are sensitive to the compound. In animal models of liver cancer with fungal infection, the ph-ph+ retards proliferation of hepatoma cells in tumor-bearing mice and remedies pneumonia and encephalitis caused by Cryptococcus neoformans. The study provides a novel therapeutic candidate for cancer patients accompanied by infection.
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Affiliation(s)
- Zizhen Zhao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Xiaorong Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Zhihong Cui
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Tingting Tong
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yingying Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yuping Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Xiaoxi Yang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Rajendiran Keerthiga
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Chen Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Ailing Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
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20
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Gao B, Zheng YT, Su AM, Sun B, Xi XG, Hou XM. Remodeling the conformational dynamics of I-motif DNA by helicases in ATP-independent mode at acidic environment. iScience 2022; 25:103575. [PMID: 34988409 PMCID: PMC8704484 DOI: 10.1016/j.isci.2021.103575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/09/2021] [Accepted: 12/03/2021] [Indexed: 01/18/2023] Open
Abstract
I-motifs are noncanonical four-stranded DNA structures formed by C-rich sequences at acidic environment with critical biofunctions. The particular pH sensitivity has inspired the development of i-motifs as pH sensors and DNA motors in nanotechnology. However, the folding and regulation mechanisms of i-motifs remain elusive. Here, using single-molecule FRET, we first show that i-motifs are more dynamic than G4s. Impressively, i-motifs display a high diversity of six folding species with slow interconversion. Further results indicate that i-motifs can be linearized by Replication protein A. More importantly, we identified a number of helicases with high specificity to i-motifs at low pH. All these helicases directly act on and efficiently resolve i-motifs into intermediates independent of ATP, although they poorly unwind G4 or duplex at low pH. Owing to the extreme sensitivity to helicases and no need for ATP, i-motif may be applied as a probe for helicase sensing both in vitro and in vivo.
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Affiliation(s)
- Bo Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ya-Ting Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ai-Min Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Gif-sur-Yvette, France
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Corresponding author
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21
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Petrunina NA, Lebedev VV, Kirillova YG, Aralov AV, Varizhuk AM, Sardushkin MV. DNA Intercalated Motifs with Non-Nucleoside Inserts. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Yu G, Niu K, Peng Y, Liu Z, Song Q, Feng Q. Large-scale screening of i-motif binding compounds in the silkworm, Bombyx mori. Biochem Biophys Res Commun 2021; 589:9-15. [PMID: 34883288 DOI: 10.1016/j.bbrc.2021.11.092] [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: 10/17/2021] [Accepted: 11/25/2021] [Indexed: 11/02/2022]
Abstract
DNA secondary structure i-motif involves in gene transcription and considered as a novel target for cancer gene therapy. I-motif-binding compounds can either stabilize or destroy the structure, resulting in change in target gene transcription. In this study, a large-scale screening of binding compounds was conducted using the i-motif structure of BmPOUM2, a transcription factor in silkworm, Bombyx mori. Surface plasmon resonance imaging (SPRi) high-throughput binding screening of 3642 compounds found 60 compounds with an binding affinity Kd of 10-7-10-6 M. SPRi and circular dichroism (CD) double screening demonstrated that the BmPOUM2 i-motif structure bound the compounds IF1, IF3, IF4, IF6 and IF7 with Kd of 10-7 M, and the compounds IF2 and tetrakis (4-N-methylpyridyl) porphine (TMPyP4) with a Kd of 10-8 M. Interestingly, IF2, IF3, IF4, IF6 and IF7 promoted the binding of the i-motif-binding protein BmILF with the i-motif structure, whereas TMPyP4 inhibited the binding. This study provided a list of compounds that have potential applications in functional analysis of i-motif structure and in pesticide and drug development through gene transcription regulation by i-motif structure.
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Affiliation(s)
- Guoxing Yu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhenming Liu
- School of Pharmacy, Peking University, Beijing, 100191, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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23
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Hur JH, Kang CY, Lee S, Parveen N, Yu J, Shamim A, Yoo W, Ghosh A, Bae S, Park CJ, Kim KK. AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation. Nucleic Acids Res 2021; 49:10150-10165. [PMID: 34469538 PMCID: PMC8464069 DOI: 10.1093/nar/gkab728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/04/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.
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Affiliation(s)
- Jeong Hwan Hur
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Chan Young Kang
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Nazia Parveen
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Amen Shamim
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.,Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Wanki Yoo
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ambarnil Ghosh
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
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24
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Cheng M, Chen J, Ju H, Zhou J, Mergny JL. Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing. J Am Chem Soc 2021; 143:7792-7807. [PMID: 33988990 DOI: 10.1021/jacs.1c02209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
i-DNA is a four-stranded, pH-sensitive structure formed by cytosine-rich DNA sequences. Previous reports have addressed the conditions for formation of this motif in DNA in vitro and validated its existence in human cells. Unfortunately, these in vitro studies have often been performed under different experimental conditions, making comparisons difficult. To overcome this, we developed a four-dimensional UV melting and annealing (4DUVMA) approach to analyze i-DNA formation under a variety of conditions (e.g., pH, temperature, salt, crowding). Analysis of 25 sequences provided a global understanding of i-DNA formation under disparate conditions, which should ultimately allow the design of accurate prediction tools. For example, we found reliable linear correlations between the midpoint of pH transition and temperature (-0.04 ± 0.003 pH unit per 1.0 °C temperature increment) and between the melting temperature and pH (-23.8 ± 1.1 °C per pH unit increment). In addition, by analyzing the hysteresis between denaturing and renaturing profiles in both pH and thermal transitions, we found that loop length, nature of the C-tracts, pH, temperature, and crowding agents all play roles in i-DNA folding kinetics. Interestingly, our data indicate which conformer is more favorable for the sequences with an odd number of cytosine base pairs. Then the thermal and pH stabilities of "native" i-DNAs from human promoter genes were measured under near physiological conditions (pH 7.0, 37 °C). The 4DUVMA method can become a universal resource to analyze the properties of any i-DNA-prone sequence.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau Cedex 91128, France
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25
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Cheng M, Qiu D, Tamon L, Ištvánková E, Víšková P, Amrane S, Guédin A, Chen J, Lacroix L, Ju H, Trantírek L, Sahakyan AB, Zhou J, Mergny J. Thermal and pH Stabilities of i‐DNA: Confronting in vitro Experiments with Models and In‐Cell NMR Data. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
- ARNA Laboratory Université de Bordeaux, INSERM U 1212, CNRS UMR5320 IECB 33607 Pessac France
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Liezel Tamon
- MRC WIMM Centre for Computational Biology MRC Weatherall Institute of Molecular Medicine Radcliffe Department of Medicine University of Oxford Oxford OX3 9DS UK
| | - Eva Ištvánková
- Central European Institute of Technology Masaryk University 62500 Brno Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology Masaryk University 62500 Brno Czech Republic
| | - Samir Amrane
- ARNA Laboratory Université de Bordeaux, INSERM U 1212, CNRS UMR5320 IECB 33607 Pessac France
| | - Aurore Guédin
- ARNA Laboratory Université de Bordeaux, INSERM U 1212, CNRS UMR5320 IECB 33607 Pessac France
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Laurent Lacroix
- IBENS Ecole Normale Supérieure CNRS INSERM PSL Research University 75005 Paris France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Lukáš Trantírek
- Central European Institute of Technology Masaryk University 62500 Brno Czech Republic
| | - Aleksandr B. Sahakyan
- MRC WIMM Centre for Computational Biology MRC Weatherall Institute of Molecular Medicine Radcliffe Department of Medicine University of Oxford Oxford OX3 9DS UK
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Jean‐Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
- ARNA Laboratory Université de Bordeaux, INSERM U 1212, CNRS UMR5320 IECB 33607 Pessac France
- Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS INSERM Institut Polytechnique de Paris 91128 Palaiseau France
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26
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Cheng M, Qiu D, Tamon L, Ištvánková E, Víšková P, Amrane S, Guédin A, Chen J, Lacroix L, Ju H, Trantírek L, Sahakyan AB, Zhou J, Mergny JL. Thermal and pH Stabilities of i-DNA: Confronting in vitro Experiments with Models and In-Cell NMR Data. Angew Chem Int Ed Engl 2021; 60:10286-10294. [PMID: 33605024 DOI: 10.1002/anie.202016801] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/22/2022]
Abstract
Recent studies indicate that i-DNA, a four-stranded cytosine-rich DNA also known as the i-motif, is actually formed in vivo; however, a systematic study on sequence effects on stability has been missing. Herein, an unprecedented number of different sequences (271) bearing four runs of 3-6 cytosines with different spacer lengths has been tested. While i-DNA stability is nearly independent on total spacer length, the central spacer plays a special role on stability. Stability also depends on the length of the C-tracts at both acidic and neutral pHs. This study provides a global picture on i-DNA stability thanks to the large size of the introduced data set; it reveals unexpected features and allows to conclude that determinants of i-DNA stability do not mirror those of G-quadruplexes. Our results illustrate the structural roles of loops and C-tracts on i-DNA stability, confirm its formation in cells, and allow establishing rules to predict its stability.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U 1212, CNRS UMR5320, IECB, 33607, Pessac, France
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Liezel Tamon
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Samir Amrane
- ARNA Laboratory, Université de Bordeaux, INSERM U 1212, CNRS UMR5320, IECB, 33607, Pessac, France
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, INSERM U 1212, CNRS UMR5320, IECB, 33607, Pessac, France
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Laurent Lacroix
- IBENS, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Aleksandr B Sahakyan
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U 1212, CNRS UMR5320, IECB, 33607, Pessac, France.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
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27
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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28
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Wu F, Niu K, Cui Y, Li C, Lyu M, Ren Y, Chen Y, Deng H, Huang L, Zheng S, Liu L, Wang J, Song Q, Xiang H, Feng Q. Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution. Commun Biol 2021; 4:98. [PMID: 33483610 PMCID: PMC7822830 DOI: 10.1038/s42003-020-01643-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/29/2020] [Indexed: 01/30/2023] Open
Abstract
G-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species. During evolution, the number, length, and density of G4s generally increased. Immunofluorescence in seven species confirmed G4s' presence and evolutionary pattern. G4s tended to cluster in chromosomes and were enriched in genetic regions. Short-loop G4s were conserved in most species, while loop-length diversity also existed, especially in mammals. The proportion of G4-bearing genes and orthologue genes, which appeared to be increasingly enriched in transcription factors, gradually increased. The antagonistic relationship between G4s and DNA methylation sites was detected. These findings imply that organisms may have evolutionarily developed G4 into a novel reversible and elaborate transcriptional regulatory mechanism benefiting multiple physiological activities of higher organisms.
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Affiliation(s)
- Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yong Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Cencen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mo Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yandong Ren
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yanfei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lihua Huang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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29
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MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif. Int J Mol Sci 2020; 22:ijms22010061. [PMID: 33374624 PMCID: PMC7793491 DOI: 10.3390/ijms22010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/23/2022] Open
Abstract
I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.
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30
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Zhang XJ, Li DD, Xu GF, Chen YQ, Zheng SC. Signal transducer and activator of transcription is involved in the expression regulation of ecdysteroid-induced insulin-like growth factor-like peptide in the pupal wing disc of silkworm, Bombyx mori. INSECT SCIENCE 2020; 27:1186-1197. [PMID: 31724818 DOI: 10.1111/1744-7917.12736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/15/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
In insects, 20-hydroxyecdysone (20E) and insulin-like growth factor-like peptides (IGFLPs) regulate the development of imaginal discs. However, how IGFLPs are up-regulated to impact the development of the pupal wing disc is still unclear. In this study, we investigated the expression regulation of IGFLP in the pupal wing disc of silkworm, Bombyx mori. We confirmed that B. mori IGFLP (BmIGFLP) was mainly expressed in the pupal wing disc and the expression of BmIGFLP could be significantly induced by 20E. Bioinformatics analysis of BmIGFLP promoter sequence revealed three cis-regulation elements (CREs) of signal transducer and activator of transcription (STAT), which is a key component in the Janus-activated kinase / STAT pathway. Luciferase activity assays showed that two CREs enhanced the transcriptional activity of BmIGFLP. Electrophoretic mobility shift and chromatin immunoprecipitation assays demonstrated that BmSTAT proteins in the nuclear extracts of B. mori pupal wing discs and BmN cells could only bind to the STAT CRE3, indicating that STAT CRE3 activated by BmSTAT enhances BmIGFLP expression at pupal stages. Although 20E could not enhance the expression of BmSTAT, 20E enhanced the nucleus translocation of BmSTAT to bind with the STAT CRE3 in the BmIGFLP promoter. The increase of transcriptional activity of the STAT CRE3 by overexpression of BmSTAT and addition of 20E in BmN cells confirmed this result. Taken together, all data indicate that BmSTAT is one of the transcription factors activating 20E-induced BmIGFLP expression in the pupal wing disc.
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Affiliation(s)
- Xiao-Juan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Dong-Dong Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guan-Feng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ya-Qing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Si-Chun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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31
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Zhang Y, El Omari K, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 2020; 48:9886-9898. [PMID: 32453431 PMCID: PMC7515729 DOI: 10.1093/nar/gkaa439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.
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Affiliation(s)
- Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
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32
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Terai Y, Sato R, Matsumura R, Iwai S, Yamamoto J. Enhanced DNA repair by DNA photolyase bearing an artificial light-harvesting chromophore. Nucleic Acids Res 2020; 48:10076-10086. [PMID: 32901252 PMCID: PMC7544235 DOI: 10.1093/nar/gkaa719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022] Open
Abstract
Photolyases are flavoenzymes responsible for the repair of carcinogenic DNA damage caused by ultraviolet radiation. They harbor the catalytic cofactor flavin adenine dinucleotide (FAD). The light-driven electron transfer from the excited state of the fully-reduced form of FAD to the DNA lesions causes rearrangement of the covalent bonds, leading to the restoration of intact nucleobases. In addition to the catalytic chromophore, some photolyases bear a secondary chromophore with better light absorption capability than FAD, acting as a light-harvesting chromophore that harvests photons in sunlight efficiently and transfers light energy to the catalytic center, as observed in natural photoreceptor proteins. Inspired by nature, we covalently and site-specifically attached a synthetic chromophore to the surface of photolyase using oligonucleotides containing a modified nucleoside and a cyclobutane-type DNA lesion, and successfully enhanced its enzymatic activity in the light-driven DNA repair. Peptide mapping in combination with theoretical calculations identified the amino acid residue that binds to the chromophore, working as an artificial light-harvesting chromophore. Our results broaden the strategies for protein engineering and provide a guideline for tuning of the light perception abilities and enzymatic activity of the photoreceptor proteins.
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Affiliation(s)
- Yuma Terai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuma Sato
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Risa Matsumura
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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33
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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34
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Chu B, Zhang D, Paukstelis PJ. A DNA G-quadruplex/i-motif hybrid. Nucleic Acids Res 2020; 47:11921-11930. [PMID: 31724696 PMCID: PMC7145706 DOI: 10.1093/nar/gkz1008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 01/23/2023] Open
Abstract
DNA can form many structures beyond the canonical Watson–Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C–C+ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.
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Affiliation(s)
- Betty Chu
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Paul J Paukstelis
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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35
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Tang W, Niu K, Yu G, Jin Y, Zhang X, Peng Y, Chen S, Deng H, Li S, Wang J, Song Q, Feng Q. In vivo visualization of the i-motif DNA secondary structure in the Bombyx mori testis. Epigenetics Chromatin 2020; 13:12. [PMID: 32138783 PMCID: PMC7059380 DOI: 10.1186/s13072-020-00334-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A large number of in vitro experiments have confirmed that DNA molecules can form i-motif advanced structure when multiple cytosines exist in the sequence. However, whether these structures are present in vivo environment still lacks sufficient experimental evidence. RESULTS In this paper, we report the in vivo visualization of i-motif structures in the nuclei and chromosomes of the testis of the invertebrate Bombyx mori using immunofluorescence staining with an antibody specifically recognizing the endogenous transcription factor BmILF, which binds i-motif structure with high specificity. The number of i-motif structures observed in the genome increased when the pH was changed from basic to acidic and decreased under treatment with an i-motif inhibitor, the porphyrin compound TMPyP4. The pH change affected the transcription of genes that contain i-motif sequences. Moreover, there were more i-motif structures observed in the testis cells in interphase than in any other cell cycle stage. CONCLUSIONS In this study, the i-motif structures in invertebrates were detected for the first time at the cell and organ levels. The formation of the structures depended on cell cycle and pH and affected gene expression.
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Affiliation(s)
- Wenhuan Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guoxing Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ying Jin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xian Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shuna Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. .,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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36
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Megalathan A, Cox BD, Wilkerson PD, Kaur A, Sapkota K, Reiner JE, Dhakal S. Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles. Nucleic Acids Res 2019; 47:7199-7212. [PMID: 31287873 PMCID: PMC6698746 DOI: 10.1093/nar/gkz565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Peter D Wilkerson
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
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37
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Niu K, Xiang L, Jin Y, Peng Y, Wu F, Tang W, Zhang X, Deng H, Xiang H, Li S, Wang J, Song Q, Feng Q. Identification of LARK as a novel and conserved G-quadruplex binding protein in invertebrates and vertebrates. Nucleic Acids Res 2019; 47:7306-7320. [PMID: 31165881 PMCID: PMC6698653 DOI: 10.1093/nar/gkz484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 12/30/2022] Open
Abstract
Double-stranded DNAs are usually present in the form of linear B-form double-helix with the base pairs of adenine (A) and thymine (T) or cytosine (C) and guanine (G), but G-rich DNA can form four-stranded G-quadruplex (G4) structures, which plays important roles in transcription, replication, translation and protection of telomeres. In this study, a RNA recognition motif (RRM)-containing protein, BmLARK, was identified and demonstrated to bind G4 structures in the promoters of a transcription factor BmPOUM2 and other three unidentified genes of Bombyx mori, as well as three well-defined G4 structures in the human genes. Homologous LARKs from Bombyx mori, Drosophila melanogaster, Mus musculus and Homo sapiens bound G4 structures in BmPOUM2 and other genes in B. mori and H. sapiens. Upon binding, LARK facilitated the formation and stability of the G4 structure, enhancing the transcription of target genes. The G4 structure was visualized in vivo in cells and testis from invertebrate B. mori and vertebrate Chinese hamster ovary (CHO) cells. The results of this study strongly suggest that LARK is a novel and conserved G4-binding protein and that the G4 structure may have developed into an elaborate epigenetic mechanism of gene transcription regulation during evolution.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lijun Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ying Jin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenhuan Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
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38
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Abou Assi H, Garavís M, González C, Damha MJ. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res 2019; 46:8038-8056. [PMID: 30124962 PMCID: PMC6144788 DOI: 10.1093/nar/gky735] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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39
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i‐Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Debnath
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Khushnood Fatma
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
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40
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019; 58:2942-2957. [PMID: 30600876 DOI: 10.1002/anie.201813288] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/27/2018] [Indexed: 12/20/2022]
Abstract
DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.
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Affiliation(s)
- Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
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41
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Furlan I, Domljanovic I, Uhd J, Astakhova K. Improving the Design of Synthetic Oligonucleotide Probes by Fluorescence Melting Assay. Chembiochem 2018; 20:587-594. [DOI: 10.1002/cbic.201800511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Ilaria Furlan
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Ivana Domljanovic
- Department of ChemistryTechnical University of Denmark Kemitorvet 206–207 2800 Kgs. Lyngby Denmark
| | - Jesper Uhd
- Department of ChemistryTechnical University of Denmark Kemitorvet 206–207 2800 Kgs. Lyngby Denmark
| | - Kira Astakhova
- Department of ChemistryTechnical University of Denmark Kemitorvet 206–207 2800 Kgs. Lyngby Denmark
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42
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Guo Z, Qin J, Zhou X, Zhang Y. Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. Int J Mol Sci 2018; 19:ijms19113691. [PMID: 30469390 PMCID: PMC6274879 DOI: 10.3390/ijms19113691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianying Qin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Xiaomao Zhou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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43
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Kaulage MH, Bhattacharya S, Muniyappa K. Structural Characterization of i-Motif Structure in the Human Acetyl-CoA Carboxylase 1 Gene Promoters and Their Role in the Regulation of Gene Expression. Chembiochem 2018; 19:1078-1087. [DOI: 10.1002/cbic.201800021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Mangesh H. Kaulage
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - K. Muniyappa
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
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