1
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Hoeher JE, Sande NE, Widom JR. Probing and perturbing riboswitch folding using a fluorescent base analogue. Photochem Photobiol 2024; 100:419-433. [PMID: 38098287 PMCID: PMC10950518 DOI: 10.1111/php.13896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 03/20/2024]
Abstract
Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ1 riboswitch consists of a stem-loop and an adenine-rich single-stranded tail ("L3"), which adopt a pseudoknot structure upon binding of the ligand preQ1 . We inserted 2-aminopurine (2-AP), a fluorescent analogue of adenine (A), into the riboswitch at six different positions within L3. Here, 2-AP functions both as a spectroscopic probe and as a "mutation" that reveals how alteration of specific A residues impacts the riboswitch. Using fluorescence and circular dichroism spectroscopy, we found that 2-AP decreases the affinity of the riboswitch for preQ1 at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ1 concentration. 2-AP substitution is most detrimental to ligand binding at sites proximal to the ligand-binding pocket, while distal labeling sites exhibit the largest impacts on the stability of the L3 domain in the absence of ligand. Insertion of multiple 2-AP residues does not induce significant additional disruptions. Our results show that interactions involving the A residues in L3 play a critical role in ligand recognition by the preQ1 riboswitch and that 2-AP substitution exerts complex and varied impacts on this riboswitch.
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Affiliation(s)
- Janson E. Hoeher
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Natalie E. Sande
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
| | - Julia R. Widom
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR
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2
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Song Y, Liu H, Xian Q, Gui C, Xu M, Zhou Y. Mechanistic insights into UHRF1‑mediated DNA methylation by structure‑based functional clarification of UHRF1 domains (Review). Oncol Lett 2023; 26:542. [PMID: 38020304 PMCID: PMC10660443 DOI: 10.3892/ol.2023.14129] [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: 03/04/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Epigenetic modification is crucial for transmitting genetic information, while abnormalities in DNA methylation modification are primarily associated with cancer and neurological diseases. As a multifunctional epigenetic modifier, ubiquitin like with PHD and ring finger domains 1 (UHRF1) mainly affects cell energy metabolism and cell cycle control. It also inhibits the transcription of tumor suppressor genes through DNA and/or histone methylation modifications, promoting the occurrence and development of cancer. Therefore, comprehensively understanding the molecular mechanism of the epigenetic modification of UHRF1 in tumors will help identify targets for inhibiting the expression and function of UHRF1. Notably, each domain of UHRF1 functions as a whole and differently. Thus, the abnormality of any domain can lead to a change in phenotype or disease. However, the specific regulatory mechanism and proteins of each domain have not been fully elucidated. The present review aimed to contribute to the study of the regulatory mechanism of UHRF1 to a greater extent in different cancers and provide ideas for drug research by clarifying the function of UHRF1 domains.
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Affiliation(s)
- Yiying Song
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Haiting Liu
- Department of Critical Care Medicine, Jinan Zhangqiu Hospital of Traditional Chinese Medicine, Jinan, Shandong 250200, P.R. China
| | - Qingqing Xian
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chengzhi Gui
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong 250012, P.R. China
| | - Mingjie Xu
- Medical Research and Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Yunying Zhou
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong 250012, P.R. China
- Medical Research and Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
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3
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Widom JR, Hoeher JE. Base-Stacking Heterogeneity in RNA Resolved by Fluorescence-Detected Circular Dichroism Spectroscopy. J Phys Chem Lett 2022; 13:8010-8018. [PMID: 35984918 PMCID: PMC9442794 DOI: 10.1021/acs.jpclett.2c01778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2022] [Indexed: 06/01/2023]
Abstract
RNA plays a critical role in many biological processes, and the structures it adopts are intimately linked to those functions. Among many factors that contribute to RNA folding, van der Waals interactions between adjacent nucleobases stabilize structures in which the bases are stacked on top of one another. Here, we utilize fluorescence-detected circular dichroism spectroscopy (FDCD) to investigate base-stacking heterogeneity in RNA labeled with the fluorescent adenine analogue 2-aminopurine (2-AP). Comparison of standard (transmission-detected) CD and FDCD spectra reveals that in dinucleotides, 2-AP fluorescence is emitted almost exclusively by unstacked molecules. In a trinucleotide, some fluorescence is emitted by a population of stacked and highly quenched molecules, but more than half originates from a minor ∼10% population of unstacked molecules. The combination of FDCD and standard CD measurements reveals the prevalence of stacked and unstacked conformational subpopulations as well as their relative fluorescence quantum yields.
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4
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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5
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Ciaco S, Gavvala K, Greiner V, Mazzoleni V, Didier P, Ruff M, Martinez-Fernandez L, Improta R, Mely Y. Thienoguanosine brightness in DNA duplexes is governed by the localization of its ππ* excitation in the lowest energy absorption band. Methods Appl Fluoresc 2022; 10. [PMID: 35472854 DOI: 10.1088/2050-6120/ac6ab6] [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: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 11/11/2022]
Abstract
Thienoguanosine (thG) is an isomorphic fluorescent guanosine (G) surrogate, which almost perfectly mimics the natural G in DNA duplexes and may therefore be used to sensitively investigate for example protein-induced local conformational changes. To fully exploit the information given by the probe, we carefully re-investigated the thG spectroscopic properties in 12-bp duplexes, when the Set and Ring Associated (SRA) domain of UHRF1 flips its 5' flanking methylcytosine (mC). The SRA-induced flipping of mC was found to strongly increase the fluorescence intensity of thG, but this increase was much larger when thG was flanked in 3' by a C residue as compared to an A residue. Surprisingly, the quantum yield and fluorescence lifetime values of thG were nearly constant, regardless of the presence of SRA and the nature of the 3' flanking residue, suggesting that the differences in fluorescence intensities might be related to changes in absorption properties. We evidenced that thG lowest energy absorption band in the duplexes can be deconvoluted into two bands peaking at ~350 nm and ~310 nm, respectively red-shifted and blue-shifted, compared to the spectrum of thG monomer. Using quantum mechanical calculations, we attributed the former to a nearly pure * excitation localized on thG and the latter to excited states with charge transfer character. The amplitude of thG red-shifted band strongly increased when its 3' flanking C residue was replaced by an A residue in the free duplex, or when its 5' flanking mC residue was flipped by SRA. As only the species associated with the red-shifted band were found to be emissive, the highly unusual finding of this work is that the brightness of thG in free duplexes as well as its changes on SRA-induced mC flipping almost entirely depend on the relative population and/or absorption coefficient of the red-shifted absorbing species.
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Affiliation(s)
- Stefano Ciaco
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Krishna Gavvala
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Vanille Greiner
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Viola Mazzoleni
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Pascal Didier
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Marc Ruff
- IGBMC, University of Strasbourg, 1 Rue Laurent Fries, 67400 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Lara Martinez-Fernandez
- Departamento de Química, Universidad Autónoma de Madrid, Facultad de Ciencias and Institute for Advanced Research in Chemistry, Madrid, Madrid, 28049, SPAIN
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini Consiglio Nazionale delle Ricerche, Consiglio Nazionale delle Ricerche, Napoli, Campania, 80134, ITALY
| | - Yves Mely
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
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6
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Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C, Antes I. Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. PLoS One 2020; 15:e0229144. [PMID: 32084194 PMCID: PMC7034832 DOI: 10.1371/journal.pone.0229144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/30/2020] [Indexed: 01/24/2023] Open
Abstract
The multi-domain protein UHRF1 is essential for DNA methylation maintenance and binds DNA via a base-flipping mechanism with a preference for hemi-methylated CpG sites. We investigated its binding to hemi- and symmetrically modified DNA containing either 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), or 5-carboxylcytosine (caC). Our experimental results indicate that UHRF1 binds symmetrically carboxylated and hybrid methylated/carboxylated CpG dyads in addition to its previously reported substrates. Complementary molecular dynamics simulations provide a possible mechanistic explanation of how the protein could differentiate between modification patterns. First, we observe different local binding modes in the nucleotide binding pocket as well as the protein's NKR finger. Second, both DNA modification sites are coupled through key residues within the NKR finger, suggesting a communication pathway affecting protein-DNA binding for carboxylcytosine modifications. Our results suggest a possible additional function of the hemi-methylation reader UHRF1 through binding of carboxylated CpG sites. This opens the possibility of new biological roles of UHRF1 beyond DNA methylation maintenance and of oxidised methylcytosine derivates in epigenetic regulation.
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Affiliation(s)
- Markus Schneider
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Carina Trummer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Andreas Stengl
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Peng Zhang
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Aleksandra Szwagierczak
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Christina Bauer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
- * E-mail:
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7
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Polepalli S, George SM, Valli Sri Vidya R, Rodrigues GS, Ramachandra L, Chandrashekar R, M DN, Rao PP, Pestell RG, Rao M. Role of UHRF1 in malignancy and its function as a therapeutic target for molecular docking towards the SRA domain. Int J Biochem Cell Biol 2019; 114:105558. [DOI: 10.1016/j.biocel.2019.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/30/2019] [Accepted: 06/14/2019] [Indexed: 01/07/2023]
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8
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Remington JM, McCullagh M, Kohler B. Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics. J Phys Chem B 2019; 123:2291-2304. [PMID: 30767498 DOI: 10.1021/acs.jpcb.8b12172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments. Analysis of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments. Combining MD simulations with HMSM analysis is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
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9
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Coordinated Dialogue between UHRF1 and DNMT1 to Ensure Faithful Inheritance of Methylated DNA Patterns. Genes (Basel) 2019; 10:genes10010065. [PMID: 30669400 PMCID: PMC6360023 DOI: 10.3390/genes10010065] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/22/2018] [Accepted: 01/11/2019] [Indexed: 12/19/2022] Open
Abstract
DNA methylation, catalyzed by DNA methyltransferases (DNMTs), is an epigenetic mark that needs to be faithfully replicated during mitosis in order to maintain cell phenotype during successive cell divisions. This epigenetic mark is located on the 5′-carbon of the cytosine mainly within cytosine–phosphate–guanine (CpG) dinucleotides. DNA methylation is asymmetrically positioned on both DNA strands, temporarily generating a hemi-methylated state after DNA replication. Hemi-methylation is a particular status of DNA that is recognized by ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1) through its SET- (Su(var)3-9, Enhancer-of-zeste and Trithorax) and RING-associated (SRA) domain. This interaction is considered to be involved in the recruitment of DNMT1 to chromatin in order to methylate the adequate cytosine on the newly synthetized DNA strand. The UHRF1/DNMT1 tandem plays a pivotal role in the inheritance of DNA methylation patterns, but the fine-tuning mechanism remains a mystery. Indeed, because DNMT1 experiences difficulties in finding the cytosine to be methylated, it requires the help of a guide, i.e., of UHRF1, which exhibits higher affinity for hemi-methylated DNA vs. non-methylated DNA. Two models of the UHRF1/DNMT1 dialogue were suggested to explain how DNMT1 is recruited to chromatin: (i) an indirect communication via histone H3 ubiquitination, and (ii) a direct interaction of UHRF1 with DNMT1. In the present review, these two models are discussed, and we try to show that they are compatible with each other.
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10
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Taka N, Karube I, Yoshida W. Direct Detection of Hemi-methylated DNA by SRA-fused Luciferase Based on Bioluminescence Resonance Energy Transfer. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1533022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Natsumi Taka
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo, Japan
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11
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Seio K, Kanamori T, Masaki Y. Synthesis of Fluorescent Nucleic Acids bearing Nucleobases Modified with Heteroaryl Group and Fluorophores. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology
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12
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Patnaik D, Estève PO, Pradhan S. Targeting the SET and RING-associated (SRA) domain of ubiquitin-like, PHD and ring finger-containing 1 (UHRF1) for anti-cancer drug development. Oncotarget 2018; 9:26243-26258. [PMID: 29899856 PMCID: PMC5995235 DOI: 10.18632/oncotarget.25425] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022] Open
Abstract
Ubiquitin-like containing PHD Ring Finger 1 (UHRF1) is a multi-domain protein with a methyl-DNA binding SRA (SET and RING-associated) domain, required for maintenance DNA methylation mediated by DNMT1. Primarily expressed in proliferating cells, UHRF1 is a cell-cycle regulated protein that is required for S phase entry. Furthermore, UHRF1 participates in transcriptional gene regulation by connecting DNA methylation to histone modifications. Upregulation of UHRF1 may serve as a biomarker for a variety of cancers; including breast, gastric, prostate, lung and colorectal carcinoma. To this end, overexpression of UHRF1 promotes cancer metastasis by triggering aberrant patterns of DNA methylation, and subsequently, silencing tumor suppressor genes. Various small molecule effectors of UHRF1 have been reported in the literature, although the mechanism of action may not be fully characterized. Small molecules that potentially bind to the SRA domain may affect the ability of UHRF1 to bind hemimethylated DNA; thereby reducing aberrant DNA methylation. Therefore, in a subset of cancers, small molecule UHRF1 inhibitors may restore normal gene expression and serve as useful anti-cancer therapeutics.
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13
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Seio K, Kanamori T, Masaki Y. Solvent- and environment-dependent fluorescence of modified nucleobases. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Bronner C, Mousli M, Burger A, Mély Y. La première étape de la transmission d’un caractère épigénétique suivie par fluorescence. Med Sci (Paris) 2017; 33:717-719. [DOI: 10.1051/medsci/20173308010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Ashraf W, Ibrahim A, Alhosin M, Zaayter L, Ouararhni K, Papin C, Ahmad T, Hamiche A, Mély Y, Bronner C, Mousli M. The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer. Oncotarget 2017; 8:51946-51962. [PMID: 28881702 PMCID: PMC5584303 DOI: 10.18632/oncotarget.17393] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/02/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is one of the deadliest diseases in the world causing record number of mortalities in both developed and undeveloped countries. Despite a lot of advances and breakthroughs in the field of oncology still, it is very hard to diagnose and treat the cancers at early stages. Here in this review we analyze the potential of Ubiquitin-like containing PHD and Ring Finger domain 1 (UHRF1) as a universal biomarker for cancers. UHRF1 is an important epigenetic regulator maintaining DNA methylation and histone code in the cell. It is highly expressed in a variety of cancers and is a well-known oncogene that can disrupt the epigenetic code and override the senescence machinery. Many studies have validated UHRF1 as a powerful diagnostic and prognostic tool to differentially diagnose cancer, predict the therapeutic response and assess the risk of tumor progression and recurrence. Highly sensitive, non-invasive and cost effective approaches are therefore needed to assess the level of UHRF1 in patients, which can be deployed in diagnostic laboratories to detect cancer and monitor disease progression.
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Affiliation(s)
- Waseem Ashraf
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Abdulkhaleg Ibrahim
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah, Saudi Arabia
- Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Liliyana Zaayter
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Khalid Ouararhni
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Christophe Papin
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Tanveer Ahmad
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Ali Hamiche
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Yves Mély
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch-Graffenstaden, France
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, Illkirch, France
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16
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Kilin V, Gavvala K, Barthes NPF, Michel BY, Shin D, Boudier C, Mauffret O, Yashchuk V, Mousli M, Ruff M, Granger F, Eiler S, Bronner C, Tor Y, Burger A, Mély Y. Dynamics of Methylated Cytosine Flipping by UHRF1. J Am Chem Soc 2017; 139:2520-2528. [PMID: 28112929 PMCID: PMC5335914 DOI: 10.1021/jacs.7b00154] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation patterns, which are critical for gene expression, are replicated by DNA methyltransferase 1 (DNMT1) and ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) proteins. This replication is initiated by the recognition of hemimethylated CpG sites and further flipping of methylated cytosines (mC) by the Set and Ring Associated (SRA) domain of UHRF1. Although crystallography has shed light on the mechanism of mC flipping by SRA, tools are required to monitor in real time how SRA reads DNA and flips the modified nucleobase. To accomplish this aim, we have utilized two distinct fluorescent nucleobase surrogates, 2-thienyl-3-hydroxychromone nucleoside (3HCnt) and thienoguanosine (thG), incorporated at different positions into hemimethylated (HM) and nonmethylated (NM) DNA duplexes. Large fluorescence changes were associated with mC flipping in HM duplexes, showing the outstanding sensitivity of both nucleobase surrogates to the small structural changes accompanying base flipping. Importantly, the nucleobase surrogates marginally affected the structure of the duplex and its affinity for SRA at positions where they were responsive to base flipping, illustrating their promise as nonperturbing probes for monitoring such events. Stopped-flow studies using these two distinct tools revealed the fast kinetics of SRA binding and sliding to NM duplexes, consistent with its reader role. In contrast, the kinetics of mC flipping was found to be much slower in HM duplexes, substantially increasing the lifetime of CpG-bound UHRF1, and thus the probability of recruiting DNMT1 to faithfully duplicate the DNA methylation profile. The fluorescence-based approach using these two different fluorescent nucleoside surrogates advances the mechanistic understanding of the UHRF1/DNMT1 tandem and the development of assays for the identification of base flipping inhibitors.
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Affiliation(s)
- Vasyl Kilin
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Nicolas P. F. Barthes
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Benoît Y. Michel
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Dongwon Shin
- TriLink BioTechnologies, LLC., San Diego, California 92121, United States
| | - Christian Boudier
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Olivier Mauffret
- LBPA, UMR 8113 CNRS, ENS Paris-Saclay, Université Paris Saclay, 94235 Cachan Cedex, France
| | - Valeriy Yashchuk
- Department of Physics, Kiev National Taras Shevchenko University, Kiev 01601, Ukraine
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Florence Granger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Sylvia Eiler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, Illkirch 67000, France
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272 CNRS, UniversitéCôte d’Azur, Parc Valrose, 06108 Nice Cedex 2, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Universitéde Strasbourg, Facultéde pharmacie, 74 Route du Rhin, 67401 Illkirch, France
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