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Yu H, Li F, Yang B, Qi Y, Guneri D, Chen W, Waller ZE, Li K, Ding Y. iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning. Nucleic Acids Res 2024; 52:W19-W28. [PMID: 38676949 PMCID: PMC11223794 DOI: 10.1093/nar/gkae315] [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: 02/13/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce 'iM-Seeker', an innovative computational platform designed for the prediction and evaluation of i-motifs. iM-Seeker exhibits the capability to identify potential i-motifs within DNA segments or entire genomes, calculating stability scores for each predicted i-motif based on parameters such as the cytosine tracts number, loop lengths, and sequence composition. Furthermore, the webserver leverages automated machine learning (AutoML) to effortlessly fine-tune the optimal i-motif scoring model, incorporating user-supplied experimental data and customised features. As an advanced, versatile approach, 'iM-Seeker' promises to advance genomic research, highlighting the potential of i-motifs in cell biology and therapeutic applications. The webserver is freely available at https://im-seeker.org.
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Affiliation(s)
- Haopeng Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fan Li
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Bibo Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yiman Qi
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Wenqian Chen
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Ke Li
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Yang B, Guneri D, Yu H, Wright EP, Chen W, Waller ZE, Ding Y. Prediction of DNA i-motifs via machine learning. Nucleic Acids Res 2024; 52:2188-2197. [PMID: 38364855 PMCID: PMC10954440 DOI: 10.1093/nar/gkae092] [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: 12/06/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments. However, there are no dedicated computational tools for predicting the folding status and strength of iM structures. Here, we introduce a machine learning pipeline, iM-Seeker, to predict both folding status and structural stability of DNA iMs. The programme iM-Seeker incorporates a Balanced Random Forest classifier trained on genome-wide iMab antibody-based CUT&Tag sequencing data to predict the folding status and an Extreme Gradient Boosting regressor to estimate the folding strength according to both literature biophysical data and our in-house biophysical experiments. iM-Seeker predicts DNA iM folding status with a classification accuracy of 81% and estimates the folding strength with coefficient of determination (R2) of 0.642 on the test set. Model interpretation confirms that the nucleotide composition of the C-rich sequence significantly affects iM stability, with a positive correlation with sequences containing cytosine and thymine and a negative correlation with guanine and adenine.
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Affiliation(s)
- Bibo Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dilek Guneri
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Haopeng Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Elisé P Wright
- Molecular Physiology School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797, Australia
| | - Wenqian Chen
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Zoë A E Waller
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [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: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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Miclot T, Froux A, D'Anna L, Bignon E, Grandemange S, Barone G, Monari A, Terenzi A. Understanding the Interactions of Guanine Quadruplexes with Peptides as Novel Strategies for Diagnosis or Tuning Biological Functions. Chembiochem 2023; 24:e202200624. [PMID: 36598366 DOI: 10.1002/cbic.202200624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/05/2023]
Abstract
Guanine quadruplexes (G4s) are nucleic acid structures exhibiting a complex structural behavior and exerting crucial biological functions in both cells and viruses. The specific interactions of peptides with G4s, as well as an understanding of the factors driving the specific recognition are important for the rational design of both therapeutic and diagnostic agents. In this review, we examine the most important studies dealing with the interactions between G4s and peptides, highlighting the strengths and limitations of current analytic approaches. We also show how the combined use of high-level molecular simulation techniques and experimental spectroscopy is the best avenue to design specifically tuned and selective peptides, thus leading to the control of important biological functions.
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Affiliation(s)
- Tom Miclot
- Universita di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, 90128, Palermo, Italy.,Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
| | - Aurane Froux
- Universita di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, 90128, Palermo, Italy.,Université de Lorraine and CNRS, UMR 7039 CRAN, 54000, Nancy, France
| | - Luisa D'Anna
- Universita di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, 90128, Palermo, Italy
| | - Emmanuelle Bignon
- Université de Lorraine and CNRS, UMR 7019 LPCT, 54000, Nancy, France
| | | | - Giampaolo Barone
- Universita di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, 90128, Palermo, Italy
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS, 75006, Paris, France
| | - Alessio Terenzi
- Universita di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies Viale delle Scienze, 90128, Palermo, Italy
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Frasson I. Editorial: Biology of non-canonical nucleic acids from humans to pathogens. Front Microbiol 2022; 13:981679. [PMID: 35935211 PMCID: PMC9345759 DOI: 10.3389/fmicb.2022.981679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
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