1
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Savitskaya VY, Novoselov KA, Dolinnaya NG, Monakhova MV, Snyga VG, Diatlova EA, Peskovatskova ES, Golyshev VM, Kitaeva MI, Eroshenko DA, Zvereva MI, Zharkov DO, Kubareva EA. Position-Dependent Effects of AP Sites Within an hTERT Promoter G-Quadruplex Scaffold on Quadruplex Stability and Repair Activity of the APE1 Enzyme. Int J Mol Sci 2025; 26:337. [PMID: 39796192 PMCID: PMC11720163 DOI: 10.3390/ijms26010337] [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: 11/24/2024] [Revised: 12/16/2024] [Accepted: 12/17/2024] [Indexed: 01/13/2025] Open
Abstract
Apurinic/apyrimidinic (AP) sites are endogenous DNA lesions widespread in human cells. Having no nucleobases, they are noncoding and promutagenic. AP site repair is generally initiated through strand incision by AP endonuclease 1 (APE1). Although AP sites' repair in regular B-DNA has been studied extensively, their processing in G-quadruplexes (G4s) has received much less attention. Here, we used the hTERT promoter region that is capable of forming three stacked parallel G4s to understand how AP sites can influence higher-order quadruplex folding and stability and how a G4 affects the efficiency of human APE1-mediated AP site processing. We designed a series of synthetic single- and double-stranded DNA constructs of varying lengths containing a stable AP site analog in both G- and C-rich strands at positions corresponding to somatic driver mutations. Using circular dichroism, we studied the effect of the AP site on hTERT G4 structure and stability. Bio-layer interferometry and gel-based approaches were employed to characterize APE1 binding to the designed DNA substrates and AP site processing. It was shown that (i) an AP site leads to G4 destabilization, which depends on the lesion location in the G4 scaffold; (ii) APE1 binds tightly to hTERT G4 structure but exhibits greatly reduced cleavage activity at AP sites embedded in the quadruplex; and (iii) a clear correlation was revealed between AP site-induced hTERT G4 destabilization and APE1 activity. We can hypothesize that reduced repair of AP sites in the hTERT G4 is one of the reasons for the high mutation rate in this promoter region.
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Affiliation(s)
- Viktoriia Yu. Savitskaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Kirill A. Novoselov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Mayya V. Monakhova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Viktoriia G. Snyga
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Evgeniia A. Diatlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.D.); (V.M.G.); (D.A.E.); (D.O.Z.)
| | - Elizaveta S. Peskovatskova
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Victor M. Golyshev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.D.); (V.M.G.); (D.A.E.); (D.O.Z.)
| | - Mariia I. Kitaeva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Daria A. Eroshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.D.); (V.M.G.); (D.A.E.); (D.O.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Y.S.); (N.G.D.); (V.G.S.); (M.I.K.); (M.I.Z.)
| | - Dmitry O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.A.D.); (V.M.G.); (D.A.E.); (D.O.Z.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena A. Kubareva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
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Deb S, Berei J, Miliavski E, Khan MJ, Broder TJ, Akurugo TA, Lund C, Fleming SE, Hillwig R, Ross J, Puri N. The Effects of Smoking on Telomere Length, Induction of Oncogenic Stress, and Chronic Inflammatory Responses Leading to Aging. Cells 2024; 13:884. [PMID: 38891017 PMCID: PMC11172003 DOI: 10.3390/cells13110884] [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: 02/29/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024] Open
Abstract
Telomeres, potential biomarkers of aging, are known to shorten with continued cigarette smoke exposure. In order to further investigate this process and its impact on cellular stress and inflammation, we used an in vitro model with cigarette smoke extract (CSE) and observed the downregulation of telomere stabilizing TRF2 and POT1 genes after CSE treatment. hTERT is a subunit of telomerase and a well-known oncogenic marker, which is overexpressed in over 85% of cancers and may contribute to lung cancer development in smokers. We also observed an increase in hTERT and ISG15 expression levels after CSE treatment, as well as increased protein levels revealed by immunohistochemical staining in smokers' lung tissue samples compared to non-smokers. The effects of ISG15 overexpression were further studied by quantifying IFN-γ, an inflammatory protein induced by ISG15, which showed greater upregulation in smokers compared to non-smokers. Similar changes in gene expression patterns for TRF2, POT1, hTERT, and ISG15 were observed in blood and buccal swab samples from smokers compared to non-smokers. The results from this study provide insight into the mechanisms behind smoking causing telomere shortening and how this may contribute to the induction of inflammation and/or tumorigenesis, which may lead to comorbidities in smokers.
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Affiliation(s)
- Shreya Deb
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Joseph Berei
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Edward Miliavski
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Muhammad J. Khan
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Taylor J. Broder
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Thomas A. Akurugo
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Cody Lund
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Sara E. Fleming
- Department of Pathology, UW Health SwedishAmerican Hospital, Rockford, IL 61107, USA;
| | - Robert Hillwig
- Department of Health Sciences Education, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Joseph Ross
- Department of Family and Community Medicine, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
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3
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [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: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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4
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [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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5
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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: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [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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6
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Hahm JY, Park J, Jang ES, Chi SW. 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification. Exp Mol Med 2022; 54:1626-1642. [PMID: 36266447 PMCID: PMC9636213 DOI: 10.1038/s12276-022-00822-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.
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Affiliation(s)
- Ja Young Hahm
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Jongyeun Park
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Eun-Sook Jang
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Sung Wook Chi
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02481 Republic of Korea
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7
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Cai Y, Cao H, Wang F, Zhang Y, Kapranov P. Complex genomic patterns of abasic sites in mammalian DNA revealed by a high-resolution SSiNGLe-AP method. Nat Commun 2022; 13:5868. [PMID: 36198706 PMCID: PMC9534904 DOI: 10.1038/s41467-022-33594-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 09/23/2022] [Indexed: 11/30/2022] Open
Abstract
DNA damage plays a critical role in biology and diseases; however, how different types of DNA lesions affect cellular functions is far from clear mostly due to the paucity of high-resolution methods that can map their locations in complex genomes, such as those of mammals. Here, we present the development and validation of SSiNGLe-AP method, which can map a common type of DNA damage, abasic (AP) sites, in a genome-wide and high-resolution manner. We apply this method to six different tissues of mice with different ages and human cancer cell lines. We find a nonrandom distribution of AP sites in the mammalian genome that exhibits dynamic enrichment at specific genomic locations, including single-nucleotide hotspots, and is significantly influenced by gene expression, age and tissue type in particular. Overall, these results suggest that we are only starting to understand the true complexities in the genomic patterns of DNA damage.
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Affiliation(s)
- Ye Cai
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China.
| | - Fang Wang
- 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
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, 361021, Xiamen, China.
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9
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Chen J, Hickey BL, Gao Z, Raz AAP, Hooley RJ, Zhong W. Sensing Base Modifications in Non-Canonically Folded DNA with an Optimized Host:Guest Sensing Array. ACS Sens 2022; 7:2164-2169. [PMID: 35917160 DOI: 10.1021/acssensors.2c00839] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An arrayed host:guest fluorescence sensor system can discriminate DNA G-quadruplex structures that differ only in the presence of single oxidation or methylation modification in the guanine base. These small modifications make subtle changes to G4 folding that are often not detectable by CD but induce differential fluorescence responses in the array. The sensing is functional in diluted serum and is capable of distinguishing individual modifications in DNA mixtures, providing a powerful method of detecting folding changes caused by DNA damage.
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10
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Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO. Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res 2022; 50:4127-4147. [PMID: 35325198 PMCID: PMC9023277 DOI: 10.1093/nar/gkac182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34-70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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11
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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: 16] [Impact Index Per Article: 5.3] [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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12
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Kim S, Hwang S. G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency. Genes (Basel) 2022; 13:genes13030391. [PMID: 35327946 PMCID: PMC8948836 DOI: 10.3390/genes13030391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
How and why distinct genetic alterations, such as BRCA1 mutation, promote tumorigenesis in certain tissues, but not others, remain an important issue in cancer research. The underlying mechanisms may reveal tissue-specific therapeutic vulnerabilities. Although the roles of BRCA1, such as DNA damage repair and stalled fork stabilization, obviously contribute to tumor suppression, these ubiquitously important functions cannot explain tissue-specific tumorigenesis by BRCA1 mutations. Recent advances in our understanding of the cancer genome and fundamental cellular processes on DNA, such as transcription and DNA replication, have provided new insights regarding BRCA1-associated tumorigenesis, suggesting that G-quadruplex (G4) plays a critical role. In this review, we summarize the importance of G4 structures in mutagenesis of the cancer genome and cell type-specific gene regulation, and discuss a recently revealed molecular mechanism of G4/base excision repair (BER)-mediated transcriptional activation. The latter adequately explains the correlation between the accumulation of unresolved transcriptional regulatory G4s and multi-level genomic alterations observed in BRCA1-associated tumors. In summary, tissue-specific tumorigenesis by BRCA1 deficiency can be explained by cell type-specific levels of transcriptional regulatory G4s and the role of BRCA1 in resolving it. This mechanism would provide an integrated understanding of the initiation and development of BRCA1-associated tumors.
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Affiliation(s)
- Sanghyun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
| | - Sohyun Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Sungnam 13488, Korea;
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Sungnam 13496, Korea
- Correspondence:
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13
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Zhou W, Cheng Y, Song B, Hao J, Miao W, Jia G, Li C. Cationic Porphyrin-Mediated G-Quadruplex DNA Oxidative Damage: Regulated by the Initial Interplay between DNA and TMPyP4. Biochemistry 2021; 60:3707-3713. [PMID: 34757721 DOI: 10.1021/acs.biochem.1c00557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplex (G4) ligand-induced DNA damage has been involved in many physiological functions of cells. Herein, cationic porphyrin (TMPyP4)-mediated DNA oxidation damage was investigated aiming at mitochondrial G4 DNA (mt9438) and its structural analogue of the thrombin-binding aptamer (TBA). TMPyP4 is found to stabilize TBA G4 but destabilize mt9438. For two resulting DNA-TMPyP4 assemblies, the distinct light-induced singlet oxygen (1O2) generation and the subsequent DNA damage were found. For mt9438-TMPyP4, a slower 1O2-induced DNA damage takes place and results in the formation of DNA aggregation. In contrast, 1O2 tends to promote DNA unfolding in a relatively faster rate for TBA-TMPyP4. Despite of such distinct DNA damage behavior, UV resonance Raman spectra reveal that for both mt9438-TMPyP4 and TBA-TMPyP4 the DNA damage commonly stems from the guanine-specific oxidation. Our results clearly indicate that the ligand-mediated DNA damage is strongly dependent on the initial interplay between DNA and the ligand.
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Affiliation(s)
- Wenqin Zhou
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China.,State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Bo Song
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China.,State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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14
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Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. Antioxidants (Basel) 2021; 10:antiox10121936. [PMID: 34943039 PMCID: PMC8750174 DOI: 10.3390/antiox10121936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 12/20/2022] Open
Abstract
Recurrent infection-inflammation cycles in cystic fibrosis (CF) patients generate a highly oxidative environment, leading to progressive destruction of the airway epithelia. The identification of novel modifier genes involved in oxidative stress susceptibility in the CF airways might contribute to devise new therapeutic approaches. We performed an unbiased genome-wide RNAi screen using a randomized siRNA library to identify oxidative stress modulators in CF airway epithelial cells. We monitored changes in cell viability after a lethal dose of hydrogen peroxide. Local similarity and protein-protein interaction network analyses uncovered siRNA target genes/pathways involved in oxidative stress. Further mining against public drug databases allowed identifying and validating commercially available drugs conferring oxidative stress resistance. Accordingly, a catalog of 167 siRNAs able to confer oxidative stress resistance in CF submucosal gland cells targeted 444 host genes and multiple circuitries involved in oxidative stress. The most significant processes were related to alternative splicing and cell communication, motility, and remodeling (impacting cilia structure/function, and cell guidance complexes). Other relevant pathways included DNA repair and PI3K/AKT/mTOR signaling. The mTOR inhibitor everolimus, the α1-adrenergic receptor antagonist doxazosin, and the Syk inhibitor fostamatinib significantly increased the viability of CF submucosal gland cells under strong oxidative stress pressure. Thus, novel therapeutic strategies to preserve airway cell integrity from the harsh oxidative milieu of CF airways could stem from a deep understanding of the complex consequences of oxidative stress at the molecular level, followed by a rational repurposing of existing "protective" drugs. This approach could also prove useful to other respiratory pathologies.
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15
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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: 35] [Impact Index Per Article: 8.8] [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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16
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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: 30] [Impact Index Per Article: 7.5] [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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17
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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: 167] [Impact Index Per Article: 41.8] [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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18
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Pavlova AV, Kubareva EA, Monakhova MV, Zvereva MI, Dolinnaya NG. Impact of G-Quadruplexes on the Regulation of Genome Integrity, DNA Damage and Repair. Biomolecules 2021; 11:1284. [PMID: 34572497 PMCID: PMC8472537 DOI: 10.3390/biom11091284] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
DNA G-quadruplexes (G4s) are known to be an integral part of the complex regulatory systems in both normal and pathological cells. At the same time, the ability of G4s to impede DNA replication plays a critical role in genome integrity. This review summarizes the results of recent studies of G4-mediated genomic and epigenomic instability, together with associated DNA damage and repair processes. Although the underlying mechanisms remain to be elucidated, it is known that, among the proteins that recognize G4 structures, many are linked to DNA repair. We analyzed the possible role of G4s in promoting double-strand DNA breaks, one of the most deleterious DNA lesions, and their repair via error-prone mechanisms. The patterns of G4 damage, with a focus on the introduction of oxidative guanine lesions, as well as their removal from G4 structures by canonical repair pathways, were also discussed together with the effects of G4s on the repair machinery. According to recent findings, there must be a delicate balance between G4-induced genome instability and G4-promoted repair processes. A broad overview of the factors that modulate the stability of G4 structures in vitro and in vivo is also provided here.
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Affiliation(s)
- Anzhela V. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Mayya V. Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
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19
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Zhao X, Usdin K. (Dys)function Follows Form: Nucleic Acid Structure, Repeat Expansion, and Disease Pathology in FMR1 Disorders. Int J Mol Sci 2021; 22:ijms22179167. [PMID: 34502075 PMCID: PMC8431139 DOI: 10.3390/ijms22179167] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5' UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders.
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Affiliation(s)
- Xiaonan Zhao
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
| | - Karen Usdin
- Correspondence: (X.Z.); (K.U.); Tel.: +1-301-451-6322 (X.Z.); +1-301-496-2189 (K.U.)
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20
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Müller N, Khobta A. Regulation of GC box activity by 8-oxoguanine. Redox Biol 2021; 43:101997. [PMID: 33965877 PMCID: PMC8120935 DOI: 10.1016/j.redox.2021.101997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 02/08/2023] Open
Abstract
The oxidation-induced DNA modification 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) was recently implicated in the activation and repression of gene transcription. We aimed at a systematic characterisation of the impacts of 8-oxodG on the activity of a GC box placed upstream from the RNA polymerase II core promoter. With the help of reporters carrying single synthetic 8-oxodG residues at four conserved G:C base pairs (underlined) within the 5'-TGGGCGGAGC-3' GC box sequence, we identified two modes of interference of 8-oxodG with the promoter activity. Firstly, 8-oxodG in the purine-rich (but not in the pyrimidine-rich) strand caused direct impairment of transcriptional activation. In addition, and independently of the first mechanism, 8-oxodG initiated a decline of the gene expression, which was mediated by the specific DNA glycosylase OGG1. For the different 8-oxodG positions, the magnitude of this effect reflected the excision preferences of OGG1. Thus, 8-oxodG seeded in the pyrimidine-rich strand was excised with the highest efficiency and caused the most pronounced decrease of the promoter activity. Conversely, 8-oxodG in the symmetric position within the same CpG dinucleotide, was poorly excised and induced no decline of the gene expression. Of note, abasic lesions caused gene silencing in both positions. By contrast, an uncleavable apurinic lesion in the pyrimidine-rich strand enhanced the GC box activity, suggesting that the AP endonuclease step provides a switch between the active versus repressed promoter states during base excision repair.
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Affiliation(s)
- Nadine Müller
- Unit "Responses to DNA Lesions", Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131, Germany
| | - Andriy Khobta
- Unit "Responses to DNA Lesions", Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55131, Germany; Institute of Nutritional Science, University of Jena, Jena, 07743, Germany.
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21
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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: 1.0] [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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22
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Cave JW, Willis DE. G-quadruplex regulation of neural gene expression. FEBS J 2021; 289:3284-3303. [PMID: 33905176 DOI: 10.1111/febs.15900] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures characterized by stacked tetrads of guanosine bases. These structures are widespread throughout mammalian genomic DNA and RNA transcriptomes, and prevalent across all tissues. The role of G-quadruplexes in cancer is well-established, but there has been a growing exploration of these structures in the development and homeostasis of normal tissue. In this review, we focus on the roles of G-quadruplexes in directing gene expression in the nervous system, including the regulation of gene transcription, mRNA processing, and trafficking, as well as protein translation. The role of G-quadruplexes and their molecular interactions in the pathology of neurological diseases is also examined. Outside of cancer, there has been only limited exploration of G-quadruplexes as potential intervention targets to treat disease or injury. We discuss studies that have used small-molecule ligands to manipulate G-quadruplex stability in order to treat disease or direct neural stem/progenitor cell proliferation and differentiation into therapeutically relevant cell types. Understanding the many roles that G-quadruplexes have in the nervous system not only provides critical insight into fundamental molecular mechanisms that control neurological function, but also provides opportunities to identify novel therapeutic targets to treat injury and disease.
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Affiliation(s)
- John W Cave
- InVitro Cell Research LLC, Englewood, NJ, USA
| | - Dianna E Willis
- Burke Neurological Institute, White Plains, NY, USA.,Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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23
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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24
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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: 4.8] [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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25
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Konno T, Melo EP, Chambers JE, Avezov E. Intracellular Sources of ROS/H 2O 2 in Health and Neurodegeneration: Spotlight on Endoplasmic Reticulum. Cells 2021; 10:233. [PMID: 33504070 PMCID: PMC7912550 DOI: 10.3390/cells10020233] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023] Open
Abstract
Reactive oxygen species (ROS) are produced continuously throughout the cell as products of various redox reactions. Yet these products function as important signal messengers, acting through oxidation of specific target factors. Whilst excess ROS production has the potential to induce oxidative stress, physiological roles of ROS are supported by a spatiotemporal equilibrium between ROS producers and scavengers such as antioxidative enzymes. In the endoplasmic reticulum (ER), hydrogen peroxide (H2O2), a non-radical ROS, is produced through the process of oxidative folding. Utilisation and dysregulation of H2O2, in particular that generated in the ER, affects not only cellular homeostasis but also the longevity of organisms. ROS dysregulation has been implicated in various pathologies including dementia and other neurodegenerative diseases, sanctioning a field of research that strives to better understand cell-intrinsic ROS production. Here we review the organelle-specific ROS-generating and consuming pathways, providing evidence that the ER is a major contributing source of potentially pathologic ROS.
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Affiliation(s)
- Tasuku Konno
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Eduardo Pinho Melo
- CCMAR—Centro de Ciências do Mar, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal;
| | - Joseph E. Chambers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK;
| | - Edward Avezov
- Department of Clinical Neurosciences, UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
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26
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Wu F, Niu K, Cui Y, Li C, Lyu M, Ren Y, Chen Y, Deng H, Huang L, Zheng S, Liu L, Wang J, Song Q, Xiang H, Feng Q. Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution. Commun Biol 2021; 4:98. [PMID: 33483610 PMCID: PMC7822830 DOI: 10.1038/s42003-020-01643-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/29/2020] [Indexed: 01/30/2023] Open
Abstract
G-quadruplex (G4) structures have been predicted in the genomes of many organisms and proven to play regulatory roles in diverse cellular activities. However, there is little information on the evolutionary history and distribution characteristics of G4s. Here, whole-genome characteristics of potential G4s were studied in 37 evolutionarily representative species. During evolution, the number, length, and density of G4s generally increased. Immunofluorescence in seven species confirmed G4s' presence and evolutionary pattern. G4s tended to cluster in chromosomes and were enriched in genetic regions. Short-loop G4s were conserved in most species, while loop-length diversity also existed, especially in mammals. The proportion of G4-bearing genes and orthologue genes, which appeared to be increasingly enriched in transcription factors, gradually increased. The antagonistic relationship between G4s and DNA methylation sites was detected. These findings imply that organisms may have evolutionarily developed G4 into a novel reversible and elaborate transcriptional regulatory mechanism benefiting multiple physiological activities of higher organisms.
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Affiliation(s)
- Feng Wu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yong Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Cencen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Mo Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yandong Ren
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yanfei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lihua Huang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Hui Xiang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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27
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Edwards AD, Marecki JC, Byrd AK, Gao J, Raney K. G-Quadruplex loops regulate PARP-1 enzymatic activation. Nucleic Acids Res 2021; 49:416-431. [PMID: 33313902 PMCID: PMC7797039 DOI: 10.1093/nar/gkaa1172] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 12/31/2022] Open
Abstract
G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.
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Affiliation(s)
- Andrea D Edwards
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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28
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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: 35] [Impact Index Per Article: 8.8] [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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29
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Visnes T, Benítez-Buelga C, Cázares-Körner A, Sanjiv K, Hanna BMF, Mortusewicz O, Rajagopal V, Albers JJ, Hagey DW, Bekkhus T, Eshtad S, Baquero JM, Masuyer G, Wallner O, Müller S, Pham T, Göktürk C, Rasti A, Suman S, Torres-Ruiz R, Sarno A, Wiita E, Homan EJ, Karsten S, Marimuthu K, Michel M, Koolmeister T, Scobie M, Loseva O, Almlöf I, Unterlass JE, Pettke A, Boström J, Pandey M, Gad H, Herr P, Jemth AS, El Andaloussi S, Kalderén C, Rodriguez-Perales S, Benítez J, Krokan HE, Altun M, Stenmark P, Berglund UW, Helleday T. Targeting OGG1 arrests cancer cell proliferation by inducing replication stress. Nucleic Acids Res 2020; 48:12234-12251. [PMID: 33211885 PMCID: PMC7708037 DOI: 10.1093/nar/gkaa1048] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022] Open
Abstract
Altered oncogene expression in cancer cells causes loss of redox homeostasis resulting in oxidative DNA damage, e.g. 8-oxoguanine (8-oxoG), repaired by base excision repair (BER). PARP1 coordinates BER and relies on the upstream 8-oxoguanine-DNA glycosylase (OGG1) to recognise and excise 8-oxoG. Here we hypothesize that OGG1 may represent an attractive target to exploit reactive oxygen species (ROS) elevation in cancer. Although OGG1 depletion is well tolerated in non-transformed cells, we report here that OGG1 depletion obstructs A3 T-cell lymphoblastic acute leukemia growth in vitro and in vivo, validating OGG1 as a potential anti-cancer target. In line with this hypothesis, we show that OGG1 inhibitors (OGG1i) target a wide range of cancer cells, with a favourable therapeutic index compared to non-transformed cells. Mechanistically, OGG1i and shRNA depletion cause S-phase DNA damage, replication stress and proliferation arrest or cell death, representing a novel mechanistic approach to target cancer. This study adds OGG1 to the list of BER factors, e.g. PARP1, as potential targets for cancer treatment.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7465 Trondheim,Norway
| | - Carlos Benítez-Buelga
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Varshni Rajagopal
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Julian J Albers
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tove Bekkhus
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Saeed Eshtad
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Juan Miguel Baquero
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation. University of Bath, Bath BA2 7AY, UK
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sarah Müller
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Therese Pham
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Camilla Göktürk
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Azita Rasti
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sharda Suman
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain.,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway.,Department of Environment and New Resources, SINTEF Ocean, N-7010 Trondheim, Norway
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Stella Karsten
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Karthick Marimuthu
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Judith Edda Unterlass
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Aleksandra Pettke
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Johan Boström
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Monica Pandey
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Helge Gad
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Patrick Herr
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | | | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Hans E Krokan
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway
| | - Mikael Altun
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Science for Life Laboratory, Division of Clinical Physiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, SE-221 00 Lund, Sweden
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
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30
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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: 1.2] [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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31
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Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (Δ Cp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. J Phys Chem B 2020; 124:5614-5625. [PMID: 32531155 DOI: 10.1021/acs.jpcb.0c04065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Knowledge of differences in heat capacity changes (ΔCp) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔCp of 61 ± 7 cal molbp -1 K -1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - G Eric Plum
- UNICON International, Inc. 241 Outerbelt Street, Columbus, Ohio 43213, United States
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.,The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08901, United States
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32
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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: 1.6] [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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33
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Yang H, Tang JA, Greenberg MM. Synthesis of Oligonucleotides Containing the N 6 -(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy⋅dG) Oxidative Damage Product Derived from 2'-Deoxyguanosine. Chemistry 2020; 26:5441-5448. [PMID: 32271495 DOI: 10.1002/chem.201905795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/19/2022]
Abstract
N6 -(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy⋅dG) is a major DNA lesion produced from 2'-deoxyguanosine under oxidizing conditions. Fapy⋅dG is produced from a common intermediate that leads to 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxodGuo), and in greater quantities in cells. The impact of Fapy⋅dG on DNA structure and function is much less well understood than that of 8-OxodGuo. This is largely due to the significantly greater difficulty in synthesizing oligonucleotides containing Fapy⋅dG than 8-OxodGuo. We describe a synthetic approach for preparing oligonucleotides containing Fapy⋅dG that will facilitate intensive studies of this lesion in DNA. A variety of oligonucleotides as long as 30 nucleotides are synthesized. We anticipate that the chemistry described herein will provide an impetus for a wide range of studies involving Fapy⋅dG.
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Affiliation(s)
- Haozhe Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Joel A Tang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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34
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Behmand B, Balanikas E, Martinez-Fernandez L, Improta R, Banyasz A, Baldacchino G, Markovitsi D. Potassium Ions Enhance Guanine Radical Generation upon Absorption of Low-Energy Photons by G-Quadruplexes and Modify Their Reactivity. J Phys Chem Lett 2020; 11:1305-1309. [PMID: 31967478 DOI: 10.1021/acs.jpclett.9b03667] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
G-Quadruplexes are formed by guanine rich DNA/RNA sequences in the presence of metal ions, which occupy the central cavity of these four-stranded structures. We show that these metal ions have a significant effect on the photogeneration and the reactivity of guanine radicals. Transient absorption experiments on G-quadruplexes formed by association of four TGGGGT strands in the presence of K+ reveal that the quantum yield of one-photon ionization at 266 nm (8.1 × 10-3) is twice as high as that determined in the presence of Na+. Replacement of Na+ with K+ also suppresses one reaction path involving deprotonated radicals, (G-H2)• → (G-H1)• tautomerization. Such behavior shows that the underlying mechanisms are governed by dynamical processes, controlled by the mobility of metal ions, which is higher for Na+ than for K+. These findings may contribute to our understanding of the ultraviolet-induced DNA damage and optimize optoelectronic devices based on four-stranded structures, beyond DNA.
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Affiliation(s)
- Behnaz Behmand
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Evangelos Balanikas
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Lara Martinez-Fernandez
- Departamento de Quı́mica, Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Cantoblanco , Spain
- IADCHEM, Institute for Advanced Research in Chemistry , Universidad Autónoma de Madrid , 28049 Cantoblanco , Spain
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16 , I-80134 Napoli , Italy
| | - Akos Banyasz
- Univ Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , F-69342 Lyon , France
| | - Gérard Baldacchino
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
| | - Dimitra Markovitsi
- Université Paris-Saclay , CEA, CNRS, LIDYL , F-91191 Gif-sur-Yvette , France
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35
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Gonzalez-Rivera JC, Orr AA, Engels SM, Jakubowski JM, Sherman MW, O'Connor KN, Matteson T, Woodcock BC, Contreras LM, Tamamis P. Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding. Comput Struct Biotechnol J 2020; 18:137-152. [PMID: 31988703 PMCID: PMC6965710 DOI: 10.1016/j.csbj.2019.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/02/2022] Open
Abstract
The oxidation of RNA has been implicated in the development of many diseases. Among the four ribonucleotides, guanosine is the most susceptible to oxidation, resulting in the formation of 8-oxo-7,8-dihydroguanosine (8-oxoG). Despite the limited knowledge about how cells regulate the detrimental effects of oxidized RNA, cellular factors involved in its regulation have begun to be identified. One of these factors is polynucleotide phosphorylase (PNPase), a multifunctional enzyme implicated in RNA turnover. In the present study, we have examined the interaction of PNPase with 8-oxoG in atomic detail to provide insights into the mechanism of 8-oxoG discrimination. We hypothesized that PNPase subunits cooperate to form a binding site using the dynamic SFF loop within the central channel of the PNPase homotrimer. We evolved this site using a novel approach that initially screened mutants from a library of beneficial mutations and assessed their interactions using multi-nanosecond Molecular Dynamics simulations. We found that evolving this single site resulted in a fold change increase in 8-oxoG affinity between 1.2 and 1.5 and/or selectivity between 1.5 and 1.9. In addition to the improvement in 8-oxoG binding, complementation of K12 Δpnp with plasmids expressing mutant PNPases caused increased cell tolerance to H2O2. This observation provides a clear link between molecular discrimination of RNA oxidation and cell survival. Moreover, this study provides a framework for the manipulation of modified-RNA protein readers, which has potential application in synthetic biology and epitranscriptomics.
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Affiliation(s)
- Juan C. Gonzalez-Rivera
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Sean M. Engels
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Joseph M. Jakubowski
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Mark W. Sherman
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Katherine N. O'Connor
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
| | - Tomas Matteson
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
| | - Brendan C. Woodcock
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24th Street, Stop A5000, Austin, TX 78712, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU Room 200, College Station, TX 77843, United States
- Corresponding authors at: McKetta Department of Chemical Engineering, The University of Texas, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, United States (L.M. Contreras).
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36
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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: 102] [Impact Index Per Article: 20.4] [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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37
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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: 8.8] [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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38
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Fleming AM, Zhu J, Ding Y, Burrows CJ. Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress. Nucleic Acids Res 2019; 47:5049-5060. [PMID: 30916339 PMCID: PMC6547423 DOI: 10.1093/nar/gkz207] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/09/2019] [Accepted: 03/18/2019] [Indexed: 12/25/2022] Open
Abstract
Oxidation of the guanine (G) heterocycle to 8-oxo-7,8-dihydroguanine (OG) in mammalian gene promoters was demonstrated to induce transcription. Potential G-quadruplex forming sequences (PQSs) in promoters have a high density of G nucleotides rendering them highly susceptible to oxidation and possible gene activation. The VEGF PQS with OG or an abasic site were synthesized at key locations in the SV40 or HSV-TK model promoters to determine the location dependency in the gene expression profile in human cells. The PQS location with respect to the transcription start site (TSS) and strand of occupancy (coding versus non-coding strand) are key parameters that determine the magnitude and direction in which gene expression changes with the chemically modified VEGF PQS. The greatest impact observed for OG or F in the PQS context in these promoters was within ∼200 bp of the TSS. Established PQSs found to occur naturally in a similar location relative to the TSS for possible oxidation-induced gene activation include c-MYC, KRAS, c-KIT, HIF-1α, PDGF-A and hTERT. The studies provide experimental constraints that were used to probe bioinformatic data regarding PQSs in the human genome for those that have the possibility to be redox switches for gene regulation.
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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
| | - Judy Zhu
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Yun Ding
- 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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39
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Abstract
Cellular damage produced by conditions generating oxidative stress have far-reaching implications in human disease that encompass, but are not restricted to aging, cardiovascular disease, type 2 diabetes, airway inflammation/asthma, cancer, and metabolic syndrome including visceral obesity, insulin resistance, fatty liver disease, and dyslipidemia. Although there are numerous sources and cellular targets of oxidative stress, this review will highlight literature that has investigated downstream consequences of oxidatively-induced DNA damage in both nuclear and mitochondrial genomes. The presence of such damage can in turn, directly and indirectly modulate cellular transcriptional and repair responses to such stressors. As such, the persistence of base damage can serve as a key regulator in coordinated gene-response cascades. Conversely, repair of these DNA lesions serves as both a suppressor of mutagenesis and by inference carcinogenesis, and as a signal for the cessation of ongoing oxidative stress. A key enzyme in all these processes is 8-oxoguanine DNA glycosylase (OGG1), which, via non-catalytic binding to oxidatively-induced DNA damage in promoter regions, serves as a nucleation site around which changes in large-scale regulation of inflammation-associated gene expression can occur. Further, the catalytic function of OGG1 can alter the three-dimensional structure of specialized DNA sequences, leading to changes in transcriptional profiles. This review will concentrate on adverse deleterious health effects that are associated with both the diminution of OGG1 activity via population-specific polymorphic variants and the complete loss of OGG1 in murine models. This mouse model displays diet- and age-related induction of metabolic syndrome, highlighting a key role for OGG1 in protecting against these phenotypes. Conversely, recent investigations using murine models having enhanced global expression of a mitochondrial-targeted OGG1 demonstrate that they are highly resistant to diet-induced disease. These data suggest strategies through which therapeutic interventions could be designed for reducing or limiting adverse human health consequences to these ubiquitous stressors.
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Affiliation(s)
- Harini Sampath
- Department of Nutritional Sciences and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, United States.
| | - R Stephen Lloyd
- Oregon Institute for Occupational Health Sciences, Department of Molecular and Medical Genetics, Oregon Health & Sciences University, Portland, Oregon, 97239, United States.
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40
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Fleming AM, Zhu J, Howpay Manage SA, Burrows CJ. Human NEIL3 Gene Expression Regulated by Epigenetic-Like Oxidative DNA Modification. J Am Chem Soc 2019; 141:11036-11049. [PMID: 31241930 PMCID: PMC6640110 DOI: 10.1021/jacs.9b01847] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The NEIL3 DNA repair gene is induced in cells
or animal models experiencing oxidative or inflammatory stress along
with oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in
the genome. We hypothesize that a G-rich promoter element that is
a potential G-quadruplex-forming sequence (PQS) in NEIL3 is a site for introduction of OG with epigenetic-like potential
for gene regulation. Activation occurs when OG is formed in the NEIL3 PQS located near the transcription start site. Oxidative
stress either introduced by TNFα or synthetically incorporated
into precise locations focuses the base excision repair process to
read and catalyze removal of OG via OG-glycosylase I (OGG1), yielding
an abasic site (AP). Thermodynamic studies showed that AP destabilizes
the duplex, enabling a structural transition of the sequence to a
G-quadruplex (G4) fold that positions the AP in a loop facilitated
by the NEIL3 PQS having five G runs in which the
four unmodified runs adopt a stable G4. This presents AP to apurinic/apyrimidinic
endonuclease 1 (APE1) that poorly cleaves the AP backbone in this
context according to in vitro studies, allowing the protein to function
as a trans activator of transcription. The proposal is supported by
chemical studies in cellulo and in vitro. Activation of NEIL3 expression via the proposed mechanism allows cells to respond to
mutagenic DNA damage removed by NEIL3 associated with oxidative or
inflammatory stress. Lastly, inspection of many mammalian genomes
identified conservation of the NEIL3 PQS, suggesting
this sequence was favorably selected to function as a redox switch
with OG as the epigenetic-like regulatory modification.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Judy Zhu
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Shereen A Howpay Manage
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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41
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Fleming AM, Zhu J, Ding Y, Esders S, Burrows CJ. Oxidative Modification of Guanine in a Potential Z-DNA-Forming Sequence of a Gene Promoter Impacts Gene Expression. Chem Res Toxicol 2019; 32:899-909. [PMID: 30821442 DOI: 10.1021/acs.chemrestox.9b00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One response to oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in a gene promoter is regulation of mRNA expression suggesting an epigenetic-like role for OG. A proposed mechanism involves G oxidation within a potential G-quadruplex-forming sequence (PQS) in the promoter, enabling a structural shift from B-DNA to a G-quadruplex fold (G4). When OG was located in the coding vs template strand, base excision repair led to an on/off transcriptional switch. Herein, a G-rich, potential Z-DNA-forming sequence (PZS) comprised of a d(GC) n repeat was explored to determine whether oxidation in this motif was also a transcriptional switch. Bioinformatic analysis found 1650 PZSs of length >10 nts in the human genome that were overrepresented in promoters and 5'-UTRs. Studies in human cells transfected with a luciferase reporter plasmid in which OG was synthesized in a PZS context in the promoter found that a coding strand OG increased expression and a template strand OG decreased expression. The initial base excision repair product of OG, an abasic site (AP), was also found to yield similar expression changes as OG. Biophysical studies on model Z-DNA strands found OG favored a shift in the equilibrium to Z-DNA from B-DNA, while an AP disrupted Z-DNA to favor a hairpin, placing AP in the loop where it is a poor substrate for the endonuclease APE1. Overall, the impact of OG and AP in a PZS on gene expression was similar to that in a PQS but reduced in magnitude.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Judy Zhu
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Selma Esders
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
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