1
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Cao H, Zhang Y, Song T, Xia L, Cai Y, Kapranov P. Common occurrence of hotspots of single strand DNA breaks at transcriptional start sites. BMC Genomics 2024; 25:368. [PMID: 38622509 PMCID: PMC11017599 DOI: 10.1186/s12864-024-10284-4] [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: 12/28/2023] [Accepted: 04/03/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND We recently developed two high-resolution methods for genome-wide mapping of two prominent types of DNA damage, single-strand DNA breaks (SSBs) and abasic (AP) sites and found highly complex and non-random patterns of these lesions in mammalian genomes. One salient feature of SSB and AP sites was the existence of single-nucleotide hotspots for both lesions. RESULTS In this work, we show that SSB hotspots are enriched in the immediate vicinity of transcriptional start sites (TSSs) in multiple normal mammalian tissues, however the magnitude of enrichment varies significantly with tissue type and appears to be limited to a subset of genes. SSB hotspots around TSSs are enriched on the template strand and associate with higher expression of the corresponding genes. Interestingly, SSB hotspots appear to be at least in part generated by the base-excision repair (BER) pathway from the AP sites. CONCLUSIONS Our results highlight complex relationship between DNA damage and regulation of gene expression and suggest an exciting possibility that SSBs at TSSs might function as sensors of DNA damage to activate genes important for DNA damage response.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Yufei Zhang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Tianrong Song
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Lu Xia
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, 361000, Xiamen, China
| | - Ye Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Philipp Kapranov
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Xiamen, China.
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2
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Hussen AS, Kravitz HL, Freudenthal BD, Whitaker AM. Oxidative DNA damage on the VEGF G-quadruplex forming promoter is repaired via long-patch BER. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:25-39. [PMID: 37606505 PMCID: PMC10984112 DOI: 10.1002/em.22570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 08/23/2023]
Abstract
In response to oxidative damage, base excision repair (BER) enzymes perturb the structural equilibrium of the VEGF promoter between B-form and G4 DNA conformations, resulting in epigenetic-like modifications of gene expression. However, the mechanistic details remain enigmatic, including the activity and coordination of BER enzymes on the damaged G4 promoter. To address this, we investigated the ability of each BER factor to conduct its repair activity on VEGF promoter G4 DNA substrates by employing pre-steady-state kinetics assays and in vitro coupled BER assays. OGG1 was able to initiate BER on double-stranded VEGF promoter G4 DNA substrates. Moreover, pre-steady-state kinetics revealed that compared to B-form DNA, APE1 repair activity on the G4 was decreased ~two-fold and is the result of slower product release as opposed to inefficient strand cleavage. Interestingly, Pol β performs multiple insertions on G4 substrates via strand displacement DNA synthesis in contrast to a single insertion on B-form DNA. The multiple insertions inhibit ligation of the Pol β products, and hence BER is not completed on the VEGF G4 promoter substrates through canonical short-patch BER. Instead, repair requires the long-patch BER flap-endonuclease activity of FEN1 in response to the multiple insertions by Pol β prior to ligation. Because the BER proteins and their repair activities are a key part of the VEGF transcriptional enhancement in response to oxidative DNA damage of the G4 VEGF promoter, the new insights reported here on BER activity in the context of this promoter are relevant toward understanding the mechanism of transcriptional regulation.
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Affiliation(s)
- Adil S. Hussen
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Haley L. Kravitz
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Bret D. Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Amy M. Whitaker
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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3
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Fleming AM, Omaga CA, Burrows CJ. NEIL3 promoter G-quadruplex with oxidatively modified bases shows magnesium-dependent folding that stalls polymerase bypass. Biochimie 2023; 214:156-166. [PMID: 37437684 PMCID: PMC10592359 DOI: 10.1016/j.biochi.2023.07.001] [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: 06/12/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Oxidative stress unleashes reactive species capable of oxidizing 2'-deoxyguanosine (G) nucleotides in G-rich sequences of the genome, such as the potential G-quadruplex forming sequencing (PQS) in the NEIL3 gene promoter. Oxidative modification of G yields 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) that can be further oxidized to hydantoin products. Herein, OG was synthesized into the NEIL3 PQS that was allowed to fold to a G-quadruplex (G4) in K+ ion solutions with varying amounts of Mg2+ in the physiological range. The Mg2+ dependency in the oxidatively modified NEIL3 G4 to stall a replicative DNA polymerase was evaluated. The polymerase was found to stall at the G4 or OG, as well as continue to full-length extension with dependency on the location of the modification and the concentration of Mg2+. To provide some clarity on these findings, OG or the hydantoins were synthesized in model NEIL3 G4 folding sequences at the positions of the polymerase study. The model G4 sequences were allowed to fold in K+ ion solutions with varying levels of Mg2+ to identify how the presence of the divalent metal impacted G4 folding depending on the location of the modification. The presence of Mg2+ either caused the transition of the NEIL3 G4 folds from an antiparallel to parallel orientation of the strands or had no impact. Structural models are proposed to understand the findings using the literature as a guide. The biological significance of the results is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Carla A Omaga
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA.
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4
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Stitch M, Avagliano D, Graczyk D, Clark IP, González L, Towrie M, Quinn SJ. Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe. J Am Chem Soc 2023; 145:21344-21360. [PMID: 37736878 PMCID: PMC10557146 DOI: 10.1021/jacs.3c06099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 09/23/2023]
Abstract
The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.
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Affiliation(s)
- Mark Stitch
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Department
of Chemistry, Chemical Physics Theory Group, University of Toronto, 80 St. George St., Toronto, Ontario M5S 3H6, Canada
| | - Daniel Graczyk
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ian P. Clark
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
| | - Michael Towrie
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Susan J Quinn
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
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5
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Yue R, Zhou M, Li X, Xu L, Lu C, Dong Z, Lei L, Liu H, Guan G, Liu Q, Zhang XB, Song G. GSH/APE1 Cascade-Activated Nanoplatform for Imaging Therapy Resistance Dynamics and Enzyme-Mediated Adaptive Ferroptosis. ACS NANO 2023; 17:13792-13810. [PMID: 37458417 DOI: 10.1021/acsnano.3c03443] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Ferroptosis, as a type of programmed cell death process, enables effective damage to various cancer cells. However, we discovered that persistent oxidative stress during ferroptosis can upregulate the apurinic/apyrimidinic endonuclease 1 (APE1) protein that induces therapeutic resistance ("ferroptosis resistance"), resulting in an unsatisfactory treatment outcome. To address APE1-induced therapeutic resistance, we developed a GSH/APE1 cascade activated therapeutic nanoplatform (GAN). Specifically, the GAN is self-assembled by DNA-functionalized ultrasmall iron oxide nanoparticles and further loaded with drug molecules (drug-GAN). GSH-triggered GAN disassembly can "turn on" the catalysis of GAN to induce efficient lipid peroxidation (LPO) for ferroptosis toward the tumor, which could upregulate APE1 expression. Subsequently, upregulated APE1 can further trigger accurate drug release for overcoming ferroptosis resistance and inducing the recovery of near-infrared fluorescence for imaging the dynamics of APE1. Importantly, adaptive drug release can overcome the adverse effects of APE1 upregulation by boosting intracellular ROS yield and increasing DNA damage, to offset APE1's functions of antioxidant and DNA repair, thus leading to adaptive ferroptosis. Moreover, with overexpressed GSH and upregulated APE1 in the tumor as stimuli, the therapeutic specificity of ferroptosis toward the tumor is greatly improved, which minimized nonspecific activation of catalysis and excessive drug release in normal tissues. Furthermore, a switchable MRI contrast from negative to positive is in sync with ferroptosis activation, which is beneficial for monitoring the ferroptosis process. Therefore, this adapted imaging and therapeutic nanoplatform can not only deliver GSH/APE1-activated lipid peroxide mediated adaptive synergistic therapy but also provided a switchable MRI/dual-channel fluorescence signal for monitoring ferroptosis activation, drug release, and therapy resistance dynamics in vivo, leading to high-specificity and high-efficiency adaptive ferroptosis therapy.
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Affiliation(s)
- Renye Yue
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Mengjie Zhou
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Xu Li
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Li Xu
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Chang Lu
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Zhe Dong
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Lingling Lei
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Huiyi Liu
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Guoqiang Guan
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Qin Liu
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Xiao-Bing Zhang
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
| | - Guosheng Song
- The State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410000, China
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Osifová Z, Šála M, Dračínský M. Hydrogen-Bonding Interactions of 8-Substituted Purine Derivatives. ACS OMEGA 2023; 8:25538-25548. [PMID: 37483191 PMCID: PMC10357537 DOI: 10.1021/acsomega.3c03244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
Abstract
Hydrogen bonding between nucleobases is a crucial noncovalent interaction for life on Earth. Canonical nucleobases form base pairs according to two main geometries: Watson-Crick pairing, which enables the static functions of nucleic acids, such as the storing of genetic information; and Hoogsteen pairing, which facilitates the dynamic functions of these biomacromolecules. This precisely tuned system can be affected by oxidation or substitution of nucleobases, leading to changes in their hydrogen-bonding patterns. This paper presents an investigation into the intermolecular interactions of various 8-substituted purine derivatives with their hydrogen-bonding partners. The systems were analyzed using nuclear magnetic resonance spectroscopy and density functional theory calculations. Our results demonstrate that the stability of hydrogen-bonded complexes, or base pairs, depends primarily on the number of intermolecular H-bonds and their donor-acceptor alternation. No strong preferences for a particular geometry, either Watson-Crick or Hoogsteen, were found.
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Affiliation(s)
- Zuzana Osifová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
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7
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Howpay Manage SA, Zhu J, Fleming AM, Burrows CJ. Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology. RSC Chem Biol 2023; 4:261-270. [PMID: 37034403 PMCID: PMC10074553 DOI: 10.1039/d2cb00233g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The DNA repair endonuclease APE1 is responsible for the cleavage of abasic sites (AP) in DNA as well as binding AP in promoter G-quadruplex (G4) folds in some genes to regulate transcription. The present studies focused on the topological properties of AP-bearing G4 folds and how they impact APE1 interaction. The human telomere sequence with a tetrahydrofuran model (F) of an AP was folded in K+- or Na+-containing buffers to adopt hybrid- or basket-folds, respectively. Endonuclease and binding assays were performed with APE1 and the G4 substrates, and the data were compared to prior work with parallel-stranded VEGF and NEIL3 promoter G4s to identify topological differences. The APE1-catalyzed endonuclease assays led to the conclusion that telomere G4 folds were slightly better substrates than the promoter G4s, but the yields were all low compared to duplex DNA. In the binding assays, G4 topological differences were observed in which APE1 bound telomere G4s with dissociation constants similar to single-stranded DNA, and promoter G4s were bound with nearly ten-fold lower values similar to duplex DNA. An in-cellulo assay with the telomere G4 in a model promoter bearing a lesion failed to regulate transcription. These data support a hypothesis that G4 topology in gene promoters is a critical feature that APE1 recognizes for gene regulation.
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Affiliation(s)
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 E. Salt Lake City UT 84112-0850 USA
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8
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Chang Y, Wu X, Lu S, Du J, Long Y, Zhu Y, Qin H. Engineered procyanidin-Fe nanoparticle alleviates intestinal inflammation through scavenging ROS and altering gut microbiome in colitis mice. Front Chem 2023; 11:1089775. [PMID: 37065822 PMCID: PMC10090317 DOI: 10.3389/fchem.2023.1089775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an idiopathic chronic inflammatory bowel disease characterized by inflammation, intestinal barrier injury, and imbalance of gut microbiota. Excess accumulation of reactive oxygen species (ROS) is closely correlated with the development and reoccurrence of IBD. Previous researches demonstrate that procyanidin, as a natural antioxidant, exhibits strong ability of eliminating ROS, thus showing good therapeutic effects in the inflammation-related diseases. Non-etheless, its poor stability and solubility always limits the therapeutic outcomes. Here, we typically designed an antioxidant coordination polymer nanoparticle using the engineering of procyanidin (Pc) and free iron (Fe), named Pc-Fe nanozyme, for effectively scavenging ROS and further inhibiting inflammation while altering the gut microbiome for the treatment of colitis. Furthermore, in vitro experiments uncover that Pc-Fe nanoparticles exert strong multi biomimic activities, including peroxidase, and glutathione peroxidase, for the scavenging of ROS and protecting cells from oxidative injury. In addition, the colon accumulation of Pc-Fe nanozyme effectively protects the intestinal mucosa from oxidative damage while significantly downregulates pro-inflammatory factors, repairs the intestinal barriers and alternates gut microbiome after orally administrated in sodium dextran sulfate (DSS) induced colitis mice. The results collectively illustrate that the multienzyme mimicking Pc-Fe nanozyme owns high potential for treating IBD through scavenging ROS, inhibiting inflammation, repairing gut barriers and alternating gut microbiome, which further promising its clinical translation on IBD treatment and other ROS induced intestinal diseases.
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Affiliation(s)
- Yongliang Chang
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Xiawei Wu
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Shengwei Lu
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Jiahao Du
- Medical School of Nantong University, Nantong, China
| | - Yixiu Long
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
| | - Yefei Zhu
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
| | - Huanlong Qin
- Shanghai Clinical College, Anhui Medical University, Shanghai, China
- The Fifth Clinical Medical College of Anhui Medical University, Hefei, China
- Department of General Surgery, School of Medicine, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
- Medical School of Nantong University, Nantong, China
- *Correspondence: Yixiu Long, ; Yefei Zhu, ; Huanlong Qin,
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9
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Ma Y, Yang Y, Xin J, He L, Hu Z, Gao T, Pan F, Guo Z. RNA G-Quadruplex within the 5'-UTR of FEN1 Regulates mRNA Stability under Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12020276. [PMID: 36829835 PMCID: PMC9952066 DOI: 10.3390/antiox12020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Reactive oxygen species (ROS) are a group of highly oxidative molecules that induce DNA damage, affecting DNA damage response (DDR) and gene expression. It is now recognized that DNA base excision repair (BER) is one of the important pathways responsible for sensing oxidative stress to eliminate DNA damage, in which FEN1 plays an important role in this process. However, the regulation of FEN1 under oxidative stress is still unclear. Here, we identified a novel RNA G-quadruplex (rG4) sequence in the 5'untranslated region (5'UTR) of FEN1 mRNA. Under oxidative stress, the G bases in the G4-forming sequence can be oxidized by ROS, resulting in structural disruption of the G-quadruplex. ROS or TMPyP4, a G4-structural ligand, disrupted the formation of G4 structure and affected the expression of FEN1. Furthermore, pull-down experiments identified a novel FEN1 rG4-binding protein, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1), and cellular studies have shown that hnRNPA1 plays an important role in regulating FEN1 expression. This work demonstrates that rG4 acts as a ROS sensor in the 5'UTR of FEN1 mRNA. Taken together, these results suggest a novel role for rG4 in translational control under oxidative stress.
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Affiliation(s)
- Ying Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yang Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingyu Xin
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Correspondence: (F.P.); (Z.G.)
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10
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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11
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Wu S, Jiang L, Lei L, Fu C, Huang J, Hu Y, Dong Y, Chen J, Zeng Q. Crosstalk between G-quadruplex and ROS. Cell Death Dis 2023; 14:37. [PMID: 36653351 PMCID: PMC9849334 DOI: 10.1038/s41419-023-05562-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.
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Affiliation(s)
- Songjiang Wu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Ling Jiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Chuhan Fu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yibo Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yumeng Dong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
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12
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Pan-Cancer Landscape of NEIL3 in Tumor Microenvironment: A Promising Predictor for Chemotherapy and Immunotherapy. Cancers (Basel) 2022; 15:cancers15010109. [PMID: 36612106 PMCID: PMC9817722 DOI: 10.3390/cancers15010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
With the aim of enhancing the understanding of NEIL3 in prognosis prediction and therapy administration, we conducted a pan-cancer landscape analysis on NEIL3. The mutation characteristics, survival patterns, and immune features of NEIL3 across cancers were analyzed. Western blotting, qPCR, and immunohistochemistry were conducted to validate the bioinformatics results. The correlation between NEIL3 and chemotherapeutic drugs, as well as immunotherapies, was estimated. NEIL3 was identified as an oncogene with prognostic value in predicting clinical outcomes in multiple cancers. Combined with the neoantigen, tumor mutational burden (TMB), and microsatellite instability (MSI) results, a strong relationship between NEIL3 and the TME was observed. NEIL3 was demonstrated to be closely associated with multiple immune parameters, including infiltrating immunocytes and pro-inflammatory chemokines, which was verified by experiments. More importantly, patients with a higher expression of NEIL3 were revealed to be more sensitive to chemotherapeutic regimens and immune checkpoint inhibitors in selected cancers, implying that NEIL3 may be an indicator for therapeutic administration. Our study indicated NEIL3 has a strong association with the immune microenvironment and phenotypic changes in certain types of cancers, which facilitated the improved understanding of NEIL3 across cancers and highlighted the potential for clinical application of NEIL3 in precision medical stratification.
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13
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Biological Functions of the DNA Glycosylase NEIL3 and Its Role in Disease Progression Including Cancer. Cancers (Basel) 2022; 14:cancers14235722. [PMID: 36497204 PMCID: PMC9737245 DOI: 10.3390/cancers14235722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation of oxidative DNA base damage can severely disrupt the integrity of the genome and is strongly associated with the development of cancer. DNA glycosylase is the critical enzyme that initiates the base excision repair (BER) pathway, recognizing and excising damaged bases. The Nei endonuclease VIII-like 3 (NEIL3) is an emerging DNA glycosylase essential in maintaining genome stability. With an in-depth study of the structure and function of NEIL3, we found that it has properties related to the process of base damage repair. For example, it not only prefers the base damage of single-stranded DNA (ssDNA), G-quadruplex and DNA interstrand crosslinks (ICLs), but also participates in the maintenance of replication fork stability and telomere integrity. In addition, NEIL3 is strongly associated with the progression of cancers and cardiovascular and neurological diseases, is incredibly significantly overexpressed in cancers, and may become an independent prognostic marker for cancer patients. Interestingly, circNEIL3, a circular RNA of exon-encoded origin by NEIL3, also promotes the development of multiple cancers. In this review, we have summarized the structure and the characteristics of NEIL3 to repair base damage. We have focused on NEIL3 and circNEIL3 in cancer development, progression and prognosis.
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14
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Yuan Y, Fu D, Xu Y, Wang X, Deng X, Zhou S, Du F, Cui X, Deng Y, Tang Z. Pt(IV) Prodrug as a Potential Antitumor Agent with APE1 Inhibitory Activity. J Med Chem 2022; 65:15344-15357. [DOI: 10.1021/acs.jmedchem.2c01318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Dingqiang Fu
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yan Xu
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xuyang Wang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiongfei Deng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shan Zhou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yun Deng
- State Key Laboratory of Southwestern Chinese Medicine Resources, The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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15
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Bangalore DM, Tessmer I. Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress. Nucleic Acids Res 2022; 50:10385-10398. [PMID: 36156093 PMCID: PMC9561264 DOI: 10.1093/nar/gkac796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The base excision repair (BER) glycosylase hOGG1 (human oxoguanine glycosylase 1) is responsible for repairing oxidative lesions in the genome, in particular oxidised guanine bases (oxoG). In addition, a role of hOGG1 in transcription regulation by recruitment of various transcription factors has been reported. Here, we demonstrate direct interactions between hOGG1 and the medically important oncogene transcription factor Myc that is involved in transcription initiation of a large number of genes including inflammatory genes. Using single molecule atomic force microscopy (AFM), we reveal recruitment of Myc to its E-box promoter recognition sequence by hOGG1 specifically under oxidative stress conditions, and conformational changes in hOGG1-Myc complexes at oxoG lesions that suggest loading of Myc at oxoG lesions by hOGG1. Importantly, our data show suppression of hOGG1 catalytic activity in oxoG repair by Myc. Furthermore, mutational analyses implicate the C28 residue in hOGG1 in oxidation induced protein dimerisation and suggest a role of hOGG1 dimerisation under oxidising conditions in hOGG1-Myc interactions. From our data we develop a mechanistic model for Myc recruitment by hOGG1 under oxidising, inflammatory conditions, which may be responsible for the observed enhanced gene expression of Myc target genes.
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Affiliation(s)
- Disha M Bangalore
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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16
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Manage SAH, Fleming AM, Chen HN, Burrows CJ. Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair. ACS Chem Biol 2022; 17:2583-2594. [PMID: 36037088 PMCID: PMC9931449 DOI: 10.1021/acschembio.2c00511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Apurinic/apyrimidinic endonuclease-1 (APE1) is a base excision repair (BER) enzyme that is also engaged in transcriptional regulation. Previous work demonstrated that the enzymatic stalling of APE1 on a promoter G-quadruplex (G4) recruits transcription factors during oxidative stress for gene regulation. Also, during oxidative stress, cysteine (Cys) oxidation is a post-translational modification (PTM) that can change a protein's function. The current study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and how this PTM at specific cysteine residues affects the function of APE1 toward the NEIL3 gene promoter G4 bearing an abasic site. Of the seven cysteine residues in APE1, five (C65, C93, C208, C296, and C310) were prone to carbonate radical anion oxidation to yield sulfenic acids that were identified and quantified by mass spectrometry. Accordingly, five Cys-to-serine (Ser) mutants of APE1 were prepared and found to have attenuated levels of endonuclease activity, depending on the position, while KD values generally decreased for G4 binding, indicating greater affinity. These data support the concept that cysteine oxidation to sulfenic acid can result in modified APE1 that enhances G4 binding at the expense of endonuclease activity during oxidative stress. Cysteine oxidation to sulfenic acid residues should be considered as one of the factors that may trigger a switch from base excision repair activity to transcriptional modulation by APE1.
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Affiliation(s)
- Shereen A. Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Hsiao-Nung Chen
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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17
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You XJ, Zhang S, Chen JJ, Tang F, He J, Wang J, Qi CB, Feng YQ, Yuan BF. Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA. Nucleic Acids Res 2022; 50:9858-9872. [PMID: 36095124 PMCID: PMC9508817 DOI: 10.1093/nar/gkac770] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/17/2022] [Accepted: 08/27/2022] [Indexed: 11/21/2022] Open
Abstract
RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
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Affiliation(s)
- Xue-Jiao You
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Shan Zhang
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Juan-Juan Chen
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Feng Tang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jingang He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chu-Bo Qi
- Department of Pathology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Yu-Qi Feng
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Department of Radiation and Medical Oncology, Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China.,Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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18
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Wang KB, Liu Y, Li Y, Dickerhoff J, Li J, Yang MH, Yang D, Kong LY. Oxidative Damage Induces a Vacancy G-Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G-Quadruplex in the Oxidized BLM Gene Promoter. J Am Chem Soc 2022; 144:6361-6372. [PMID: 35352895 PMCID: PMC9904417 DOI: 10.1021/jacs.2c00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Guanine (G)-oxidation to 8-oxo-7,8-dihydroguanine (OG) by reactive oxygen species in genomic DNA has been implicated with various human diseases. G-quadruplex (G4)-forming sequences in gene promoters are highly susceptible to G-oxidation, which can subsequently cause gene activation. However, the underlying G4 structural changes that result from OG modifications remain poorly understood. Herein, we investigate the effect of G-oxidation on the BLM gene promoter G4. For the first time, we show that OG can induce a G-vacancy-containing G4 (vG4), which can be filled in and stabilized by guanine metabolites and derivatives. We determined the NMR solution structure of the cGMP-fill-in oxidized BLM promoter vG4. This is the first complex structure of an OG-induced vG4 from a human gene promoter sequence with a filled-in guanine metabolite. The high-resolution structure elucidates the structural features of the specific 5'-end cGMP-fill-in for the OG-induced vG4. Interestingly, the OG is removed from the G-core and becomes part of the 3'-end capping structure. A series of guanine metabolites and derivatives are evaluated for fill-in activity to the oxidation-induced vG4. Significantly, cellular guanine metabolites, such as cGMP and GTP, can bind and stabilize the OG-induced vG4, suggesting their potential regulatory role in response to oxidative damage in physiological and pathological processes. Our work thus provides exciting insights into how oxidative damage and cellular metabolites may work together through a G4-based epigenetic feature for gene regulation. Furthermore, the NMR structure can guide the rational design of small-molecule inhibitors that specifically target the oxidation-induced vG4s.
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Affiliation(s)
| | | | - Yipu Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Jonathan Dickerhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinzhu Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Ming-Hua Yang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Department of Chemistry, and Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People’s Republic of China
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19
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Fleming AM, Burrows CJ. Chemistry of ROS-mediated oxidation to the guanine base in DNA and its biological consequences. Int J Radiat Biol 2022; 98:452-460. [PMID: 34747670 PMCID: PMC8881305 DOI: 10.1080/09553002.2021.2003464] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE One outcome of DNA damage from hydroxyl radical generated by ionizing radiation (IR) or by the Fenton reaction is oxidation of the nucleobases, especially guanine (G). While 8-oxo-7,8-dihydroguanine (OG) is a commonly studied oxidized lesion, several others are formed in high abundance, including 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), a prevalent product in in vitro chemistry that is challenging to study from cellular sources. In this short review, we have a goal of explaining new insights into hydroxyl radical-induced oxidation chemistry of G in DNA and comparing it to endogenous DNA damage, as well as commenting on the biological outcomes of DNA base damage. CONCLUSIONS Pathways of oxidation of G are discussed and a comparison is made between IR (hydroxyl radical chemistry) and endogenous oxidative stress that largely forms carbonate radical anion as a reactive intermediate. These pathways overlap with the formation of OG and 2Ih, but other guanine-derived lesions are more pathway specific. The biological consequences of guanine oxidation include both mutagenesis and epigenetics; a new mechanism of gene regulation via the base excision repair pathway is described for OG, whereas the impact of IR in forming guanine modifications may be to confound this process in addition to introduction of mutagenic sites.
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20
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Fleming AM, Manage SAH, Burrows CJ. Binding of AP endonuclease-1 to G-quadruplex DNA depends on the N-terminal domain, Mg 2+ and ionic strength. ACS BIO & MED CHEM AU 2021; 1:44-56. [PMID: 35005714 DOI: 10.1021/acsbiomedchemau.1c00031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base excision repair enzyme apurinic/apyrimidinic endonuclease-1 (APE1) is also engaged in transcriptional regulation. APE1 can function in both pathways when the protein binds to a promoter G-quadruplex (G4) bearing an abasic site (modeled with tetrahydrofuran, F) that leads to enzymatic stalling on the non-canonical fold to recruit activating transcription factors. Biochemical and biophysical studies to address APE1's binding and catalytic activity with the vascular endothelial growth factor (VEGF) promoter G4 are lacking, and the present work provides insight on this topic. Herein, the native APE1 was used for cleavage assays, and the catalytically inactive mutant D210A was used for binding assays with double-stranded DNA (dsDNA) versus the native G4 or the G4 with F at various positions, revealing dependencies of the interaction on the cation concentrations K+ and Mg2+ and the N-terminal domain of the protein. Assays in 0, 1, or 10 mM Mg2+ found that dsDNA and G4 substrates required the cation for both binding and catalysis, in which G4 binding increased with [Mg2+]. Studies with 50 versus physiological 140 mM K+ ions showed that F-containing dsDNA was bound and cleaved by APE1; whereas, the G4s with F were poorly cleaved in low salt and not cleaved at all at higher salt while the binding remained robust. Using Δ33 or Δ61 N-terminal truncated APE1 proteins, the binding and cleavage of dsDNA with F was minimally impacted; in contrast, the G4s required the N-terminus for binding and catalysis is nearly abolished without the N-terminus. With this knowledge, we found APE1 could remodel the F-containing VEGF promoter dsDNA→G4 folds in solution. Lastly, the addition of the G4 ligand pyridostatin inhibited APE1 binding and cleavage of F-containing G4s but not dsDNA. The biological and medicinal chemistry implications of the results are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Shereen A Howpay Manage
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, UT 84112-0850, United States
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21
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Linke R, Limmer M, Juranek SA, Heine A, Paeschke K. The Relevance of G-Quadruplexes for DNA Repair. Int J Mol Sci 2021; 22:12599. [PMID: 34830478 PMCID: PMC8620898 DOI: 10.3390/ijms222212599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/28/2023] Open
Abstract
DNA molecules can adopt a variety of alternative structures. Among these structures are G-quadruplex DNA structures (G4s), which support cellular function by affecting transcription, translation, and telomere maintenance. These structures can also induce genome instability by stalling replication, increasing DNA damage, and recombination events. G-quadruplex-driven genome instability is connected to tumorigenesis and other genetic disorders. In recent years, the connection between genome stability, DNA repair and G4 formation was further underlined by the identification of multiple DNA repair proteins and ligands which bind and stabilize said G4 structures to block specific DNA repair pathways. The relevance of G4s for different DNA repair pathways is complex and depends on the repair pathway itself. G4 structures can induce DNA damage and block efficient DNA repair, but they can also support the activity and function of certain repair pathways. In this review, we highlight the roles and consequences of G4 DNA structures for DNA repair initiation, processing, and the efficiency of various DNA repair pathways.
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Affiliation(s)
- Rebecca Linke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michaela Limmer
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Stefan A. Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127 Bonn, Germany; (R.L.); (M.L.); (S.A.J.); (A.H.)
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22
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Impact of Chromatin Dynamics and DNA Repair on Genomic Stability and Treatment Resistance in Pediatric High-Grade Gliomas. Cancers (Basel) 2021; 13:cancers13225678. [PMID: 34830833 PMCID: PMC8616465 DOI: 10.3390/cancers13225678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, due in great part to treatment resistance driven by complex DNA repair mechanisms. pHGGs have recently been divided into molecular subtypes based on mutations affecting the N-terminal tail of the histone variant H3.3 and the ATRX/DAXX histone chaperone that deposits H3.3 at repetitive heterochromatin loci that are of paramount importance to the stability of our genome. This review addresses the functions of H3.3 and ATRX/DAXX in chromatin dynamics and DNA repair, as well as the impact of mutations affecting H3.3/ATRX/DAXX on treatment resistance and how the vulnerabilities they expose could foster novel therapeutic strategies. Abstract Despite their low incidence, pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine gliomas (DIPGs), are the leading cause of mortality in pediatric neuro-oncology. Recurrent, mutually exclusive mutations affecting K27 (K27M) and G34 (G34R/V) in the N-terminal tail of histones H3.3 and H3.1 act as key biological drivers of pHGGs. Notably, mutations in H3.3 are frequently associated with mutations affecting ATRX and DAXX, which encode a chaperone complex that deposits H3.3 into heterochromatic regions, including telomeres. The K27M and G34R/V mutations lead to distinct epigenetic reprogramming, telomere maintenance mechanisms, and oncogenesis scenarios, resulting in distinct subgroups of patients characterized by differences in tumor localization, clinical outcome, as well as concurrent epigenetic and genetic alterations. Contrasting with our understanding of the molecular biology of pHGGs, there has been little improvement in the treatment of pHGGs, with the current mainstays of therapy—genotoxic chemotherapy and ionizing radiation (IR)—facing the development of tumor resistance driven by complex DNA repair pathways. Chromatin and nucleosome dynamics constitute important modulators of the DNA damage response (DDR). Here, we summarize the major DNA repair pathways that contribute to resistance to current DNA damaging agent-based therapeutic strategies and describe the telomere maintenance mechanisms encountered in pHGGs. We then review the functions of H3.3 and its chaperones in chromatin dynamics and DNA repair, as well as examining the impact of their mutation/alteration on these processes. Finally, we discuss potential strategies targeting DNA repair and epigenetic mechanisms as well as telomere maintenance mechanisms, to improve the treatment of pHGGs.
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Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine. Int J Mol Sci 2021; 22:ijms222011025. [PMID: 34681690 PMCID: PMC8539351 DOI: 10.3390/ijms222011025] [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: 09/07/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Stepwise oxidation of the epigenetic mark 5-methylcytosine and base excision repair (BER) of the resulting 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) may provide a mechanism for reactivation of epigenetically silenced genes; however, the functions of 5-fC and 5-caC at defined gene elements are scarcely explored. We analyzed the expression of reporter constructs containing either 2′-deoxy-(5-fC/5-caC) or their BER-resistant 2′-fluorinated analogs, asymmetrically incorporated into CG-dinucleotide of the GC box cis-element (5′-TGGGCGGAGC) upstream from the RNA polymerase II core promoter. In the absence of BER, 5-caC caused a strong inhibition of the promoter activity, whereas 5-fC had almost no effect, similar to 5-methylcytosine or 5-hydroxymethylcytosine. BER of 5-caC caused a transient but significant promoter reactivation, succeeded by silencing during the following hours. Both responses strictly required thymine DNA glycosylase (TDG); however, the silencing phase additionally demanded a 5′-endonuclease (likely APE1) activity and was also induced by 5-fC or an apurinic/apyrimidinic site. We propose that 5-caC may act as a repressory mark to prevent premature activation of promoters undergoing the final stages of DNA demethylation, when the symmetric CpG methylation has already been lost. Remarkably, the downstream promoter activation or repression responses are regulated by two separate BER steps, where TDG and APE1 act as potential switches.
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Fleming AM, Burrows CJ. Oxidative stress-mediated epigenetic regulation by G-quadruplexes. NAR Cancer 2021; 3:zcab038. [PMID: 34541539 PMCID: PMC8445369 DOI: 10.1093/narcan/zcab038] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023] Open
Abstract
Many cancer-associated genes are regulated by guanine (G)-rich sequences that are capable of refolding from the canonical duplex structure to an intrastrand G-quadruplex. These same sequences are sensitive to oxidative damage that is repaired by the base excision repair glycosylases OGG1 and NEIL1–3. We describe studies indicating that oxidation of a guanosine base in a gene promoter G-quadruplex can lead to up- and downregulation of gene expression that is location dependent and involves the base excision repair pathway in which the first intermediate, an apurinic (AP) site, plays a key role mediated by AP endonuclease 1 (APE1/REF1). The nuclease activity of APE1 is paused at a G-quadruplex, while the REF1 capacity of this protein engages activating transcription factors such as HIF-1α, AP-1 and p53. The mechanism has been probed by in vitro biophysical studies, whole-genome approaches and reporter plasmids in cellulo. Replacement of promoter elements by a G-quadruplex sequence usually led to upregulation, but depending on the strand and precise location, examples of downregulation were also found. The impact of oxidative stress-mediated lesions in the G-rich sequence enhanced the effect, whether it was positive or negative.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA
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25
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Robinson J, Raguseo F, Nuccio SP, Liano D, Di Antonio M. DNA G-quadruplex structures: more than simple roadblocks to transcription? Nucleic Acids Res 2021; 49:8419-8431. [PMID: 34255847 PMCID: PMC8421137 DOI: 10.1093/nar/gkab609] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple 'off switches' for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.
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Affiliation(s)
- Jenna Robinson
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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Miclot T, Corbier C, Terenzi A, Hognon C, Grandemange S, Barone G, Monari A. Forever Young: Structural Stability of Telomeric Guanine Quadruplexes in the Presence of Oxidative DNA Lesions*. Chemistry 2021; 27:8865-8874. [PMID: 33871121 DOI: 10.1002/chem.202100993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 01/13/2023]
Abstract
Human telomeric DNA, in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine (8oxoG) lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.
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Affiliation(s)
- Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy.,Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Camille Corbier
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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Bielskutė S, Plavec J, Podbevšek P. Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter. Nucleic Acids Res 2021; 49:2346-2356. [PMID: 33638996 PMCID: PMC7913773 DOI: 10.1093/nar/gkab057] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/08/2021] [Accepted: 01/22/2021] [Indexed: 01/08/2023] Open
Abstract
Misregulation of BCL2 expression has been observed with many diseases and is associated with cellular exposure to reactive oxygen species. A region upstream of the P1 promoter in the human BCL2 gene plays a major role in regulating transcription. This G/C-rich region is highly polymorphic and capable of forming G-quadruplex structures. Herein we report that an oxidative event simulated with an 8-oxo-7,8-dihydroguanine (oxoG) substitution within a long G-tract results in a reduction of structural polymorphism. Surprisingly, oxoG within a 25-nt construct boosts thermal stability of the resulting G-quadruplex. This is achieved by distinct hydrogen bonding properties of oxoG, which facilitate formation of an antiparallel basket-type G-quadruplex with a three G-quartet core and a G·oxoG·C base triad. While oxoG has previously been considered detrimental for G-quadruplex formation, its stabilizing effect within a promoter described in this study suggests a potential novel regulatory role of oxidative stress in general and specifically in BCL2 gene transcription.
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Affiliation(s)
- Stasė Bielskutė
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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29
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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30
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Bordin DL, Lirussi L, Nilsen H. Cellular response to endogenous DNA damage: DNA base modifications in gene expression regulation. DNA Repair (Amst) 2021; 99:103051. [PMID: 33540225 DOI: 10.1016/j.dnarep.2021.103051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022]
Abstract
The integrity of the genetic information is continuously challenged by numerous genotoxic insults, most frequently in the form of oxidation, alkylation or deamination of the bases that result in DNA damage. These damages compromise the fidelity of the replication, and interfere with the progression and function of the transcription machineries. The DNA damage response (DDR) comprises a series of strategies to deal with DNA damage, including transient transcriptional inhibition, activation of DNA repair pathways and chromatin remodeling. Coordinated control of transcription and DNA repair is required to safeguardi cellular functions and identities. Here, we address the cellular responses to endogenous DNA damage, with a particular focus on the role of DNA glycosylases and the Base Excision Repair (BER) pathway, in conjunction with the DDR factors, in responding to DNA damage during the transcription process. We will also discuss functions of newly identified epigenetic and regulatory marks, such as 5-hydroxymethylcytosine and its oxidative products and 8-oxoguanine, that were previously considered only as DNA damages. In light of these resultsthe classical perception of DNA damage as detrimental for cellular processes are changing. and a picture emerges whereDNA glycosylases act as dynamic regulators of transcription, placing them at the intersection of DNA repair and gene expression modulation.
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Affiliation(s)
- Diana L Bordin
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Lisa Lirussi
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway.
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31
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Sengupta A, Roy SS, Chowdhury S. Non-duplex G-Quadruplex DNA Structure: A Developing Story from Predicted Sequences to DNA Structure-Dependent Epigenetics and Beyond. Acc Chem Res 2021; 54:46-56. [PMID: 33347280 DOI: 10.1021/acs.accounts.0c00431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The story of the non-duplex DNA form known as the G-quadruplex (G4) has traversed a winding path. From initial skepticism followed by debate to a surge in interest, the G4 story intertwines many threads. Starting with computational predictions of a gene regulatory role, which now include epigenetic functions, our group was involved in many of these advances along with many other laboratories. Following a brief background, set in the latter half of the last century when the concept of the G4 as a structure took ground, here we account the developments. This is through a lens that though focused on our groups' research presents work from many other groups that played significant roles. Together these provide a broad perspective to the G4 story. Initially we were intrigued on seeing potential G4 (pG4)-forming sequences, then known to be found primarily at the telomeres and immunoglobin switch regions, occurring throughout the genome and being particularly prevalent in promoters of bacteria. We further observed that pG4s were not only prevalent but also conserved through evolution in promoters of human, chimpanzee, mouse and rat genomes. This was between 2005 and 2007. Encouraged by these partly and partly in response to the view held by many that genome-wide presence of G4s were genomic "accidents", the focus shifted to seeking experimental evidence.In the next year, 2008, two independent findings showed promise. First, on treating human cancer cells with G4-binding ligands, we observed widespread change in gene expression. Second, our search for the missing G4-specific transcription factor, without which, importantly, G4s in promoters posed only half the story, yielded results. We determined how NM23-H2 (also known as NME2 or NDPK-B) interacts with G4s and how interaction of NM23-H2 with a G4 in the promoter of the oncogene c-myc was important for regulation of c-myc transcription. NM23-H2, and subsequently many other similar factors discovered by multiple groups, is possibly giving shape to what might be the "G4-transcriptome". Later, a close look at NM23-H2-G4 interaction in regulation of the human reverse transcriptase gene (hTERT) revealed the role of G4s in local epigenetic modifications. Meanwhile work from others showed how G4s impact histone modifications following replication. Together these show the intrinsic role of DNA sequence, through formation of DNA structure, in epigenetics.More recent work, however, was waiting to reveal aspects that tend to bring forth a completely new understanding of G4s. We observed that the telomere-repeat-binding-factor-2 (TRF2), known canonically to be telomere-associated, binds extensively outside telomeres throughout the genome. Moreover, a large fraction of the non-telomeric TRF2 sites comprise G4s. Second, the extent of non-telomeric TRF2 binding at promoters was dependent on telomere length. Thereby TRF2-induced epigenetic gene regulation was telomere-dependent. Together these implicate underlying connections that show signs of addressing an intriguing unanswered question that takes us back to the beginning: Why are G4s prevalent in two distinct regions, the telomeres and gene promoters?
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Affiliation(s)
- Antara Sengupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shuvra Shekhar Roy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shantanu Chowdhury
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Gorini F, Scala G, Cooke MS, Majello B, Amente S. Towards a comprehensive view of 8-oxo-7,8-dihydro-2'-deoxyguanosine: Highlighting the intertwined roles of DNA damage and epigenetics in genomic instability. DNA Repair (Amst) 2021; 97:103027. [PMID: 33285475 PMCID: PMC7926032 DOI: 10.1016/j.dnarep.2020.103027] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a major product of DNA oxidation, is a pre-mutagenic lesion which is prone to mispair, if left unrepaired, with 2'-deoxyadenosine during DNA replication. While unrepaired or incompletely repaired 8-oxodG has classically been associated with genome instability and cancer, it has recently been reported to have a role in the epigenetic regulation of gene expression. Despite the growing collection of genome-wide 8-oxodG mapping studies that have been used to provide new insight on the functional nature of 8-oxodG within the genome, a comprehensive view that brings together the epigenetic and the mutagenic nature of the 8-oxodG is still lacking. To help address this gap, this review aims to provide (i) a description of the state-of-the-art knowledge on both the mutagenic and epigenetic roles of 8-oxodG; (ii) putative molecular models through which the 8-oxodG can cause genome instability; (iii) a possible molecular model on how 8-oxodG, acting as an epigenetic signal, could cause the translocations and deletions which are associated with cancer.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Barbara Majello
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy.
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Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
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Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
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Wang K, Maayah M, Sweasy JB, Alnajjar KS. The role of cysteines in the structure and function of OGG1. J Biol Chem 2020; 296:100093. [PMID: 33203705 PMCID: PMC7948458 DOI: 10.1074/jbc.ra120.016126] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022] Open
Abstract
8-Oxoguanine glycosylase (OGG1) is a base excision repair enzyme responsible for the recognition and removal of 8-oxoguanine, a commonly occurring oxidized DNA modification. OGG1 prevents the accumulation of mutations and regulates the transcription of various oxidative stress–response genes. In addition to targeting DNA, oxidative stress can affect proteins like OGG1 itself, specifically at cysteine residues. Previous work has shown that the function of OGG1 is sensitive to oxidants, with the cysteine residues of OGG1 being the most likely site of oxidation. Due to the integral role of OGG1 in maintaining cellular homeostasis under oxidative stress, it is important to understand the effect of oxidants on OGG1 and the role of cysteines in its structure and function. In this study, we investigate the role of the cysteine residues in the function of OGG1 by mutating and characterizing each cysteine residue. Our results indicate that the cysteines in OGG1 fall into four functional categories: those that are necessary for (1) glycosylase activity (C146 and C255), (2) lyase activity (C140S, C163, C241, and C253), and (3) structural stability (C253) and (4) those with no known function (C28 and C75). These results suggest that under conditions of oxidative stress, cysteine can be targeted for modifications, thus altering the response of OGG1 and affecting its downstream cellular functions.
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Affiliation(s)
- Katarina Wang
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Marah Maayah
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, The University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Khadijeh S Alnajjar
- Department of Cellular and Molecular Medicine, The University of Arizona Cancer Center, Tucson, Arizona, USA.
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Abstract
Cellular DNA is constantly chemically altered by exogenous and endogenous agents. As all processes of life depend on the transmission of the genetic information, multiple biological processes exist to ensure genome integrity. Chemically damaged DNA has been linked to cancer and aging, therefore it is of great interest to map DNA damage formation and repair to elucidate the distribution of damage on a genome-wide scale. While the low abundance and inability to enzymatically amplify DNA damage are obstacles to genome-wide sequencing, new developments in the last few years have enabled high-resolution mapping of damaged bases. Recently, a number of DNA damage sequencing library construction strategies coupled to new data analysis pipelines allowed the mapping of specific DNA damage formation and repair at high and single nucleotide resolution. Strikingly, these advancements revealed that the distribution of DNA damage is heavily influenced by chromatin states and the binding of transcription factors. In the last seven years, these novel approaches have revealed new genomic maps of DNA damage distribution in a variety of organisms as generated by diverse chemical and physical DNA insults; oxidative stress, chemotherapeutic drugs, environmental pollutants, and sun exposure. Preferred sequences for damage formation and repair have been elucidated, thus making it possible to identify persistent weak spots in the genome as locations predicted to be vulnerable for mutation. As such, sequencing DNA damage will have an immense impact on our ability to elucidate mechanisms of disease initiation, and to evaluate and predict the efficacy of chemotherapeutic drugs.
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Affiliation(s)
- Cécile Mingard
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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36
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Zafar M, Hazeslip L, Chauhan MZ, Byrd AK. The Expression of Human DNA Helicase B Is Affected by G-Quadruplexes in the Promoter. Biochemistry 2020; 59:2401-2409. [PMID: 32478505 PMCID: PMC7346868 DOI: 10.1021/acs.biochem.0c00218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/26/2020] [Indexed: 12/25/2022]
Abstract
G-Quadruplexes are secondary structures that can form in guanine-rich DNA and RNA that have been implicated in regulating multiple biological processes, including transcription. G-Quadruplex-forming sequences are prevalent in promoter regions of proto-oncogenes and DNA repair proteins. HELB is a human helicase involved in DNA replication and repair with 12 runs of three to four guanines in the proximal promoter. This sequence has the potential to form three canonical three-tetrad G-quadruplexes. Our results show that although all three G-quadruplexes can form, a structure containing two noncanonical G-quadruplexes with longer loops containing runs of three to four guanines is the most prevalent. These HELB G-quadruplexes are stable under physiological conditions. In cells, stabilization of the G-quadruplexes results in a decrease in the level of HELB expression, suggesting that the G-quadruplexes in the HELB promoter serve as transcriptional repressors.
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Affiliation(s)
- Maroof
Khan Zafar
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Lindsey Hazeslip
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Muhammad Zain Chauhan
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Alicia K. Byrd
- Department
of Biochemistry and Molecular Biology, University
of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Winthrop
P. Rockefeller Cancer Institute, Little Rock, Arkansas 72205, United States
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37
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Fleming AM, Zhu J, Jara-Espejo M, Burrows CJ. Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2'-Deoxyguanosine. Biochemistry 2020; 59:2616-2626. [PMID: 32567845 DOI: 10.1021/acs.biochem.0c00387] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequences of DNA typically adopt B-form duplexes in genomes, although noncanonical structures such as G-quadruplexes, i-motifs, Z-DNA, and cruciform structures can occur. A challenge is to determine the functions of these various structures in cellular processes. We and others have hypothesized that G-rich G-quadruplex-forming sequences in human genome promoters serve to sense oxidative damage generated during oxidative stress impacting gene regulation. Herein, chemical tools and a cell-based assay were used to study the oxidation of guanine to 8-oxo-7,8-dihydroguanine (OG) in the context of a cruciform-forming sequence in a gene promoter to determine the impact on transcription. We found that OG in the nontemplate strand in the loop of a cruciform-forming sequence could induce gene expression; conversely when OG was in the same sequence on the template strand, gene expression was inhibited. A model for the transcriptional changes observed is proposed in which OG focuses the DNA repair process on the promoter to impact expression. Our cellular and biophysical studies and literature sources support the idea that removal of OG from duplex DNA by OGG1 yields an abasic site (AP) that triggers a structural shift to the cruciform fold. The AP-bearing cruciform structure is presented to APE1, which functions as a conduit between DNA repair and gene regulation. The significance is enhanced by a bioinformatic study of all human gene promoters and transcription termination sites for inverted repeats (IRs). Comparison of the two regions showed that promoters have stable and G-rich IRs at a low frequency and termination sites have many AT-rich IRs with low stability.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Manuel Jara-Espejo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States.,Department of Morphology, Piracicaba Dental School, University of Campinas-UNICAMP, Av. Limeira 901, Piracicaba, CEP 13414-018 Sao Paulo, Brazil
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Reina C, Cavalieri V. Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures. Int J Mol Sci 2020; 21:E4172. [PMID: 32545267 PMCID: PMC7312119 DOI: 10.3390/ijms21114172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.
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Affiliation(s)
- Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, 90127 Palermo, Italy;
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
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Fleming AM, Burrows CJ. Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters. J Am Chem Soc 2020; 142:1115-1136. [PMID: 31880930 PMCID: PMC6988379 DOI: 10.1021/jacs.9b11050] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living in an oxygen atmosphere demands an ability to thrive in the presence of reactive oxygen species (ROS). Aerobic organisms have successfully found solutions to the oxidative threats imposed by ROS by evolving an elaborate detoxification system, upregulating ROS during inflammation, and utilizing ROS as messenger molecules. In this Perspective, recent studies are discussed that demonstrate ROS as signaling molecules for gene regulation by combining two emergent properties of the guanine (G) heterocycle in DNA, namely, oxidation sensitivity and a propensity for G-quadruplex (G4) folding, both of which depend upon sequence context. In human gene promoters, this results from an elevated 5'-GG-3' dinucleotide frequency and GC enrichment near transcription start sites. Oxidation of DNA by ROS drives conversion of G to 8-oxo-7,8-dihydroguanine (OG) to mark target promoters for base excision repair initiated by OG-glycosylase I (OGG1). Sequence-dependent mechanisms for gene activation are available to OGG1 to induce transcription. Either OGG1 releases OG to yield an abasic site driving formation of a non-canonical fold, such as a G4, to be displayed to apurinic/apyrimidinic 1 (APE1) and stalling on the fold to recruit activating factors, or OGG1 binds OG and facilitates activator protein recruitment. The mechanisms described drive induction of stress response, DNA repair, or estrogen-induced genes, and these pathways are novel potential anticancer targets for therapeutic intervention. Chemical concepts provide a framework to discuss the regulatory or possible epigenetic potential of the OG modification in DNA, in which DNA "damage" and non-canonical folds collaborate to turn on or off gene expression. The next steps for scientific discovery in this growing field are discussed.
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Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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40
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Giorgio M, Dellino GI, Gambino V, Roda N, Pelicci PG. On the epigenetic role of guanosine oxidation. Redox Biol 2020; 29:101398. [PMID: 31926624 PMCID: PMC6926346 DOI: 10.1016/j.redox.2019.101398] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 01/14/2023] Open
Abstract
Chemical modifications of DNA and RNA regulate genome functions or trigger mutagenesis resulting in aging or cancer. Oxidations of macromolecules, including DNA, are common reactions in biological systems and often part of regulatory circuits rather than accidental events. DNA alterations are particularly relevant since the unique role of nuclear and mitochondrial genome is coding enduring and inheritable information. Therefore, an alteration in DNA may represent a relevant problem given its transmission to daughter cells. At the same time, the regulation of gene expression allows cells to continuously adapt to the environmental changes that occur throughout the life of the organism to ultimately maintain cellular homeostasis. Here we review the multiple ways that lead to DNA oxidation and the regulation of mechanisms activated by cells to repair this damage. Moreover, we present the recent evidence suggesting that DNA damage caused by physiological metabolism acts as epigenetic signal for regulation of gene expression. In particular, the predisposition of guanine to oxidation might reflect an adaptation to improve the genome plasticity to redox changes.
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Affiliation(s)
- Marco Giorgio
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Valentina Gambino
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Niccolo' Roda
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Via Adamello 16, 20139, Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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41
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Terenzi A, Gattuso H, Spinello A, Keppler BK, Chipot C, Dehez F, Barone G, Monari A. Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy. Antioxidants (Basel) 2019; 8:antiox8100472. [PMID: 31658666 PMCID: PMC6826623 DOI: 10.3390/antiox8100472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 01/24/2023] Open
Abstract
The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.
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Affiliation(s)
- Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, Spain.
| | - Hugo Gattuso
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Angelo Spinello
- CNR-IOM DEMOCRITOS c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
| | - Christophe Chipot
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
| | - Giampaolo Barone
- Dipartimento di Scienze Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy.
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
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