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Rosenkrantz JL, Brandorff JE, Raghib S, Kapadia A, Vaine CA, Bragg DC, Farmiloe G, Jacobs FMJ. ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP). Proc Natl Acad Sci U S A 2024; 121:e2401217121. [PMID: 39102544 DOI: 10.1073/pnas.2401217121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a severe neurodegenerative disorder resulting from an inherited intronic SINE-Alu-VNTR (SVA) retrotransposon in the TAF1 gene that causes dysregulation of TAF1 transcription. The specific mechanism underlying this dysregulation remains unclear, but it is hypothesized to involve the formation of G-quadruplexes (G4) structures within the XDP-SVA that impede transcription. In this study, we show that ZNF91, a critical repressor of SVA retrotransposons, specifically binds to G4-forming DNA sequences. Further, we found that genetic deletion of ZNF91 exacerbates the molecular phenotype associated with the XDP-SVA insertion in patient cells, while no difference was observed when ZNF91 was deleted from isogenic control cells. Additionally, we observed a significant age-related reduction in ZNF91 expression in whole blood and brain, indicating a progressive loss of repression of the XDP-SVA in XDP. These findings indicate that ZNF91 plays a crucial role in controlling the molecular phenotype associated with XDP. Since ZNF91 binds to G4-forming DNA sequences in SVAs, this suggests that interactions between ZNF91 and G4-forming sequences in the XDP-SVA minimize the severity of the molecular phenotype. Our results showing that ZNF91 expression levels significantly decrease with age provide a potential explanation for the age-related progressive neurodegenerative character of XDP. Collectively, our study provides important insights into the protective role of ZNF91 in XDP pathogenesis and suggests that restoring ZNF91 expression, destabilization of G4s, or targeted repression of the XDP-SVA could be future therapeutic strategies to prevent or treat XDP.
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Affiliation(s)
- Jimi L Rosenkrantz
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - J Elias Brandorff
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Sanaz Raghib
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Ashni Kapadia
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Christine A Vaine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA 02129
| | - D Cristopher Bragg
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Boston, MA 02129
| | - Grace Farmiloe
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Frank M J Jacobs
- Faculty of Science, Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
- Faculty of Science, Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
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2
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Moura NMM, Guedes S, Salvador D, Oliveira H, Alves MQ, Paradis N, Wu C, Neves MGPMS, Ramos CIV. Oncogenic and telomeric G-quadruplexes: Targets for porphyrin-triphenylphosphonium conjugates. Int J Biol Macromol 2024; 277:134126. [PMID: 39097044 DOI: 10.1016/j.ijbiomac.2024.134126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
DNA chains with sequential guanine (G) repeats can lead to the formation of G-quadruplexes (G4), which are found in functional DNA and RNA regions like telomeres and oncogene promoters. The development of molecules with adequate structural features to selectively stabilize G4 structures can counteract cell immortality, highly described for cancer cells, and also downregulate transcription events underlying cell apoptosis and/or senescence processes. We describe here, the efficiency of four highly charged porphyrins-phosphonium conjugates to act as G4 stabilizing agents. The spectrophotometric results allowed to select the conjugates P2-PPh3 and P3-PPh3 as the most promising ones to stabilize selectively G4 structures. Molecular dynamics simulation experiments were performed and support the preferential binding of P2-PPh3 namely to MYC and of P3-PPh3 to KRAS. The ability of both ligands to block the activity of Taq polymerase was confirmed and also their higher cytotoxicity against the two melanoma cell lines A375 and SK-MEL-28 than to immortalized skin keratinocytes. Both ligands present efficient cellular uptake, nuclear co-localization and high ability to generate 1O2 namely when interacting with G4 structure. The obtained data points the synthesized porphyrins as promising ligands to be used in a dual approach that can combine G4 stabilization and Photodynamic therapy (PDT).
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Affiliation(s)
- Nuno M M Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sofia Guedes
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Diana Salvador
- CESAM-Centre for Environmental and Marine Studies, Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; CICECO, Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Helena Oliveira
- CESAM-Centre for Environmental and Marine Studies, Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mariana Q Alves
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, United States of America
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, United States of America
| | - M Graça P M S Neves
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Catarina I V Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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3
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Bhatt U, Cucchiarini A, Luo Y, Evans CW, Mergny JL, Iyer KS, Smith NM. Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA. Genome Res 2024; 34:217-230. [PMID: 38355305 PMCID: PMC10984386 DOI: 10.1101/gr.278236.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNAs in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was confirmed in vitro using biophysical experiments under near-physiological conditions. We find that the majority of the tested pG4s form highly stable G4 structures, and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences are able to form iM structures, consistent with the idea that RNA is unable to form stable iMs. Unexpectedly, these C-rich sequences instead form Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and underexplored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNAs, and show G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering the understanding of the structure-function relationship in lncRNAs.
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Affiliation(s)
- Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
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4
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Moura NMM, Cavaleiro JAS, Neves MGPMS, Ramos CIV. opp-Dibenzoporphyrin Pyridinium Derivatives as Potential G-Quadruplex DNA Ligands. Molecules 2023; 28:6318. [PMID: 37687146 PMCID: PMC10489911 DOI: 10.3390/molecules28176318] [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: 07/12/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 09/10/2023] Open
Abstract
Since the occurrence of tumours is closely associated with the telomerase function and oncogene expression, the structure of such enzymes and genes are being recognized as targets for new anticancer drugs. The efficacy of several ligands in telomerase inhibition and in the regulation of genes expression, by an effective stabilisation of G-quadruplexes (G4) DNA structures, is being considered as a promising strategy in cancer therapies. When evaluating the potential of a ligand for telomerase inhibition, the selectivity towards quadruplex versus duplex DNA is a fundamental attribute due to the large amount of double-stranded DNA in the cellular nucleus. This study reports the evaluated efficacy of three tetracationic opp-dibenzoporphyrins, a free base, and the corresponding zinc(II) and nickel(II) complexes, to stabilise G4 structures, namely the telomeric DNA sequence (AG3(T2AG3)3). In order to evaluate the selectivity of these ligands towards G4 structures, their interaction towards DNA calf thymus, as a double-strand DNA sequence, were also studied. The data obtained by using different spectroscopic techniques, such as ultraviolet-visible, fluorescence, and circular dichroism, suggested good affinity of the free-base porphyrin and of its zinc(II) complex for the considered DNA structures, both showing a pattern of selectivity for the telomeric G4 structure. A pattern of aggregation in aqueous solution was detected for both Zn(II) and Ni(II) metallo dibenzoporphyrins and the ability of DNA sequences to induce ligand disaggregation was observed.
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Affiliation(s)
- Nuno M. M. Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (J.A.S.C.); (M.G.P.M.S.N.)
| | | | | | - Catarina I. V. Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (J.A.S.C.); (M.G.P.M.S.N.)
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5
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Jedlička P, Tokan V, Kejnovská I, Hobza R, Kejnovský E. Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species. Mob DNA 2023; 14:3. [PMID: 37038191 PMCID: PMC10088271 DOI: 10.1186/s13100-023-00291-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Canonical telomeres (telomerase-synthetised) are readily forming G-quadruplexes (G4) on the G-rich strand. However, there are examples of non-canonical telomeres among eukaryotes where telomeric tandem repeats are invaded by specific retrotransposons. Drosophila melanogaster represents an extreme example with telomeres composed solely by three retrotransposons-Het-A, TAHRE and TART (HTT). Even though non-canonical telomeres often show strand biased G-distribution, the evidence for the G4-forming potential is limited. RESULTS Using circular dichroism spectroscopy and UV absorption melting assay we have verified in vitro G4-formation in the HTT elements of D. melanogaster. Namely 3 in Het-A, 8 in TART and 2 in TAHRE. All the G4s are asymmetrically distributed as in canonical telomeres. Bioinformatic analysis showed that asymmetric distribution of potential quadruplex sequences (PQS) is common in telomeric retrotransposons in other Drosophila species. Most of the PQS are located in the gag gene where PQS density correlates with higher DNA sequence conservation and codon selection favoring G4-forming potential. The importance of G4s in non-canonical telomeres is further supported by analysis of telomere-associated retrotransposons from various eukaryotic species including green algae, Diplomonadida, fungi, insects and vertebrates. Virtually all analyzed telomere-associated retrotransposons contained PQS, frequently with asymmetric strand distribution. Comparison with non-telomeric elements showed independent selection of PQS-rich elements from four distinct LINE clades. CONCLUSION Our findings of strand-biased G4-forming motifs in telomere-associated retrotransposons from various eukaryotic species support the G4-formation as one of the prerequisites for the recruitment of specific retrotransposons to chromosome ends and call for further experimental studies.
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Affiliation(s)
- Pavel Jedlička
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
| | - Iva Kejnovská
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic
| | - Eduard Kejnovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200, Brno, Czech Republic.
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6
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Makova KD, Weissensteiner MH. Noncanonical DNA structures are drivers of genome evolution. Trends Genet 2023; 39:109-124. [PMID: 36604282 PMCID: PMC9877202 DOI: 10.1016/j.tig.2022.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023]
Abstract
In addition to the canonical right-handed double helix, other DNA structures, termed 'non-B DNA', can form in the genomes across the tree of life. Non-B DNA regulates multiple cellular processes, including replication and transcription, yet its presence is associated with elevated mutagenicity and genome instability. These discordant cellular roles fuel the enormous potential of non-B DNA to drive genomic and phenotypic evolution. Here we discuss recent studies establishing non-B DNA structures as novel functional elements subject to natural selection, affecting evolution of transposable elements (TEs), and specifying centromeres. By highlighting the contributions of non-B DNA to repeated evolution and adaptation to changing environments, we conclude that evolutionary analyses should include a perspective of not only DNA sequence, but also its structure.
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Affiliation(s)
- Kateryna D Makova
- Department of Biology, Penn State University, 310 Wartik Laboratory, University Park, PA 16802, USA.
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7
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Deng Z, Zhang Y, Gao C, Shen W, Wang S, Ni X, Liu S, Li X. A transposon-introduced G-quadruplex motif is selectively retained and constrained to downregulate CYP321A1. INSECT SCIENCE 2022; 29:1629-1642. [PMID: 35226400 DOI: 10.1111/1744-7917.13021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Insects utilize xenobiotic compounds to up- and downregulate cytochrome P450 monooxygenases (P450s) involved in detoxification of toxic xenobiotics including phytochemicals and pesticides. G-quadruplexes (G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes. Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored. Here, we show that CYP321A1, a xenobiotic-metabolizing P450 from Helicoverpa zea, a polyphagous insect of economic importance, has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region. The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K+ . The G4 ligand N-methylmesoporphyrin IX (NMM) strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2. The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.
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Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Chao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wei Shen
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Shan Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinzhi Ni
- USDA-ARS, Crop Genetics and Breeding Research Unit, University of Georgia, Tifton Campus, Tifton, GA, USA
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Science, Huazhong Agricultural University, Wuhan, China
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, USA
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8
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Vannutelli A, Perreault JP, Ouangraoua A. G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content. NAR Genom Bioinform 2022; 4:lqac010. [PMID: 35261973 PMCID: PMC8896161 DOI: 10.1093/nargab/lqac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/06/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
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Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
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9
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I. V. Ramos C, A. S. Almodôvar V, Candeias N, Santos T, Cruz C, Graça P. M. S. Neves M, Tomé AC. Diketopyrrolo[3,4–c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures. Bioorg Chem 2022; 122:105703. [DOI: 10.1016/j.bioorg.2022.105703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
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10
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Stefos GC, Theodorou G, Politis I. Genomic landscape, polymorphism and possible LINE-associated delivery of G-quadruplex motifs in the bovine genes. Genomics 2022; 114:110272. [PMID: 35092818 DOI: 10.1016/j.ygeno.2022.110272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/29/2022]
Abstract
G-Quadruplex structures are non-B DNA structures that occur in regions carrying short runs of guanines. They are implicated in several biological processes including transcription, translation, replication and telomere maintenance as well as in several pathological conditions like cancer and thus they have gained the attention of the scientific community. The rise of the -omics era significantly affected the G-quadruplex research and the genome-wide characterization of G-Quadruplexes has been rendered a necessary first step towards applying genomics approaches for their study. While in human and several model organisms there is a considerable number of works studying genome-wide the DNA motifs with potential to form G-quadruplexes (G4-motifs), there is a total absence of any similar studies regarding livestock animals. The objectives of the present study were to provide a detailed characterization of the bovine genic G4-motifs' distribution and properties and to suggest a possible mechanism for the delivery of G4 motifs in the genes. Our data indicate that the distribution of G4-motifs within bovine genes and the annotation of said genes to Gene Ontology terms are similar to what is already shown for other organisms. By investigating their structural characteristics and polymorphism, it is obvious that the overall stability of the putative quadruplex structures is in line with the current notion in the G4 field. Similarly to human, the bovine G4-motifs are overrepresented in specific LINE repeat elements, the L1_BTs in the case of cattle. We highlight the potential role of these elements as vehicles for delivery of G4 motifs in the introns of the bovine genes. Lastly, it seems that a basis exists for connecting traits of agricultural importance to the genetic variation of G4 motifs, thus, the value of cattle as an interesting new model organism for G4-related genetic studies might be worth to be investigated.
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Affiliation(s)
- Georgios C Stefos
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece.
| | - Georgios Theodorou
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece.
| | - Ioannis Politis
- Agricultural University of Athens, Department of Animal Science, Laboratory of Animal Breeding & Husbandry, 75 Iera Odos, 118 55, Athens, Greece
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11
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Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
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12
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Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Mol Biol Evol 2021; 37:3576-3600. [PMID: 32722770 DOI: 10.1093/molbev/msaa194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.
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Affiliation(s)
- Di Chen
- Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA.,Department of Operations and Decision Systems, Université Laval, Québec, Canada
| | - Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA.,EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.,The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA
| | - Kateryna D Makova
- The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
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Tokan V, Lorenzo JLR, Jedlicka P, Kejnovska I, Hobza R, Kejnovsky E. Quadruplex-Forming Motif Inserted into 3'UTR of Ty1his3-AI Retrotransposon Inhibits Retrotransposition in Yeast. BIOLOGY 2021; 10:347. [PMID: 33924086 PMCID: PMC8074290 DOI: 10.3390/biology10040347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
Abstract
Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3'UTR of Ty1his3-AI retrotransposon and measured the frequency of retrotransposition in yeast strains BY4741, Y00509 (without Pif1 helicase) and with G4-stabilization by N-methyl mesoporphyrin IX (NMM) treatment. We evaluated the impact of G4s on mRNA levels by RT-qPCR and products of reverse transcription by Southern blot analysis. We found that the presence of G4 inhibited Ty1his3-AI retrotransposition. The effect was stronger when G4s were on a transcription template strand which leads to reverse transcription interruption. Both NMM and Pif1p deficiency reduced the retrotransposition irrespective of the presence of a G4 motif in the Ty1his3-AI element. Quantity of mRNA and products of reverse transcription did not fully explain the impact of G4s on Ty1his3-AI retrotransposition indicating that G4s probably affect some other steps of the retrotransposon life-cycle (e.g., translation, VLP formation, integration). Our results suggest that G4 DNA conformation can tune the activity of mobile genetic elements that in turn contribute to shaping the eukaryotic genomes.
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Affiliation(s)
- Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Jose Luis Rodriguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Iva Kejnovska
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic;
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
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Kharel P, Becker G, Tsvetkov V, Ivanov P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res 2020; 48:12534-12555. [PMID: 33264409 PMCID: PMC7736831 DOI: 10.1093/nar/gkaa1126] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.
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Affiliation(s)
- Prakash Kharel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gertraud Becker
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Tsvetkov
- Computational Oncology Group, I. M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Federal Research and Clinical Center for Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 117912, Russia
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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15
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Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA. G-quadruplex structures bind to EZ-Tn5 transposase. Biochimie 2020; 177:190-197. [PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
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Affiliation(s)
- Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Eng Wee Chua
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Jennifer Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.
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Sjakste T, Leonova E, Petrovs R, Trapina I, Röder MS, Sjakste N. Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ 2020; 8:e8569. [PMID: 32110488 PMCID: PMC7034378 DOI: 10.7717/peerj.8569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.
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Affiliation(s)
- Tatjana Sjakste
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Elina Leonova
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Ilva Trapina
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Marion S Röder
- Leibniz Institute for Plant Genetics and Crop Research, Gatersleben, Germany
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Gianfrancesco O, Geary B, Savage AL, Billingsley KJ, Bubb VJ, Quinn JP. The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. Int J Mol Sci 2019; 20:ijms20235977. [PMID: 31783611 PMCID: PMC6928650 DOI: 10.3390/ijms20235977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most recently evolved class of retrotransposable elements, found solely in primates, including humans. SVAs are preferentially found at genic, high GC loci, and have been termed "mobile CpG islands". We hypothesise that the ability of SVAs to mobilise, and their non-random distribution across the genome, may result in differential regulation of certain pathways. We analysed SVA distribution patterns across the human reference genome and identified over-representation of SVAs at zinc finger gene clusters. Zinc finger proteins are able to bind to and repress SVA function through transcriptional and epigenetic mechanisms, and the interplay between SVAs and zinc fingers has been proposed as a major feature of genome evolution. We describe observations relating to the clustering patterns of both reference SVAs and polymorphic SVA insertions at zinc finger gene loci, suggesting that the evolution of this network may be ongoing in humans. Further, we propose a mechanism to direct future research and validation efforts, in which the interplay between zinc fingers and their epigenetic modulation of SVAs may regulate a network of zinc finger genes, with the potential for wider transcriptional consequences.
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Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bethany Geary
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Abigail L. Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Kimberley J. Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- Correspondence:
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18
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Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 PMCID: PMC6745008 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
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Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
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Puig Lombardi E, Holmes A, Verga D, Teulade-Fichou MP, Nicolas A, Londoño-Vallejo A. Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species. Nucleic Acids Res 2019; 47:6098-6113. [PMID: 31114920 PMCID: PMC6614823 DOI: 10.1093/nar/gkz463] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/29/2022] Open
Abstract
G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.
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Affiliation(s)
| | - Allyson Holmes
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
| | - Daniela Verga
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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21
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Hon J, Martínek T, Zendulka J, Lexa M. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics 2018; 33:3373-3379. [PMID: 29077807 DOI: 10.1093/bioinformatics/btx413] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation G-quadruplexes (G4s) are one of the non-B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4-specific antibodies and G4-unwinding helicase mutants confirm this conjecture. These four-stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form. Results We describe and have tested a newly developed Bioconductor package for identifying potential quadruplex-forming sequences (PQS). The package is easy-to-use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4-seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictions was 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter. Availability and implementation http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder-1.4.1. Contact lexa@fi.muni.cz. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jirí Hon
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Tomáš Martínek
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Jaroslav Zendulka
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 61266 Brno, Czech Republic
| | - Matej Lexa
- Department of Information Technology, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic
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Tokan V, Puterova J, Lexa M, Kejnovsky E. Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. BMC Genomics 2018; 19:184. [PMID: 29510672 PMCID: PMC5838962 DOI: 10.1186/s12864-018-4563-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/20/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. RESULTS In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since "mutants" (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. CONCLUSIONS Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.
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Affiliation(s)
- Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
| | - Janka Puterova
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 61200 Brno, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic
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23
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Impact of Repetitive Elements on the Y Chromosome Formation in Plants. Genes (Basel) 2017; 8:genes8110302. [PMID: 29104214 PMCID: PMC5704215 DOI: 10.3390/genes8110302] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 12/21/2022] Open
Abstract
In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.
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24
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Hall AC, Ostrowski LA, Pietrobon V, Mekhail K. Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes. Nucleus 2017; 8:162-181. [PMID: 28406751 DOI: 10.1080/19491034.2017.1292193] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cells have evolved intricate mechanisms to maintain genome stability despite allowing mutational changes to drive evolutionary adaptation. Repetitive DNA sequences, which represent the bulk of most genomes, are a major threat to genome stability often driving chromosome rearrangements and disease. The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. Maintaining the stability of these loci is critical to overall cellular fitness and lifespan. Therefore, cells have evolved mechanisms to regulate rDNA copy number, telomere length and transposon activity, as well as DNA repair at these loci. In addition, non-canonical structure-forming DNA motifs can also modulate the function of these repetitive DNA loci by impacting their transcription, replication, and stability. Here, we discuss key mechanisms that maintain rDNA repeats, telomeres, and transposons in yeast and human before highlighting emerging roles for non-canonical DNA structures at these repetitive loci.
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Affiliation(s)
- Amanda C Hall
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Lauren A Ostrowski
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Violena Pietrobon
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Karim Mekhail
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada.,b Canada Research Chairs Program ; Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
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25
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Sahakyan AB, Murat P, Mayer C, Balasubramanian S. G-quadruplex structures within the 3' UTR of LINE-1 elements stimulate retrotransposition. Nat Struct Mol Biol 2017; 24:243-247. [PMID: 28134931 DOI: 10.1038/nsmb.3367] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/22/2016] [Indexed: 12/28/2022]
Abstract
Long interspersed nuclear elements (LINEs) are ubiquitous transposable elements in higher eukaryotes that have a significant role in shaping genomes, owing to their abundance. Here we report that guanine-rich sequences in the 3' untranslated regions (UTRs) of hominoid-specific LINE-1 elements are coupled with retrotransposon speciation and contribute to retrotransposition through the formation of G-quadruplex (G4) structures. We demonstrate that stabilization of the G4 motif of a human-specific LINE-1 element by small-molecule ligands stimulates retrotransposition.
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Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clemens Mayer
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
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26
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Moriyama K, Lai MS, Masai H. Interaction of Rif1 Protein with G-Quadruplex in Control of Chromosome Transactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:287-310. [PMID: 29357064 DOI: 10.1007/978-981-10-6955-0_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent studies on G-quadruplex (G4) revealed crucial and conserved functions of G4 in various biological systems. We recently showed that Rif1, a conserved nuclear factor, binds to G4 present in the intergenic regions and plays a major role in spatiotemporal regulation of DNA replication. Rif1 may tether chromatin fibers through binding to G4, generating specific chromatin domains that dictate the replication timing. G4 and its various binding partners are now implicated in many other chromosome regulations, including transcription, replication initiation, recombination, gene rearrangement, and transposition.
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Affiliation(s)
- Kenji Moriyama
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Mong Sing Lai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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27
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Abstract
A significant part of eukaryotic genomes is formed by transposable elements (TEs) containing not only genes but also regulatory sequences. Some of the regulatory sequences located within TEs can form secondary structures like hairpins or three-stranded (triplex DNA) and four-stranded (quadruplex DNA) conformations. This review focuses on recent evidence showing that G-quadruplex-forming sequences in particular are often present in specific parts of TEs in plants and humans. We discuss the potential role of these structures in the TE life cycle as well as the impact of G-quadruplexes on replication, transcription, translation, chromatin status, and recombination. The aim of this review is to emphasize that TEs may serve as vehicles for the genomic spread of G-quadruplexes. These non-canonical DNA structures and their conformational switches may constitute another regulatory system that, together with small and long non-coding RNA molecules and proteins, contribute to the complex cellular network resulting in the large diversity of eukaryotes.
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28
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Hall LL, Lawrence JB. RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev 2016; 37:137-147. [PMID: 27218204 DOI: 10.1016/j.gde.2016.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 11/29/2022]
Abstract
Beginning with the precedent of XIST RNA as a 'chromosomal RNA' (cRNA), there is growing interest in the possibility that a diversity of non-coding RNAs may function in chromatin. We review findings which lead us to suggest that RNA is essentially a widespread component of interphase chromosomes. Further, RNA likely contributes to architecture and regulation, with repeat-rich 'junk' RNA in euchromatin (ecRNA) promoting a more open chromatin state. Thousands of low-abundance nuclear RNAs have been reported, however it remains a challenge to determine which of these may function in chromatin. Recent findings indicate that repetitive sequences are enriched in chromosome-associated non-coding RNAs, and repeat-rich RNA shows unusual properties, including localization and stability, with similarities to XIST RNA. We suggest two frontiers in genome biology are emerging and may intersect: the broad contribution of RNA to interphase chromosomes and the distinctive properties of repeat-rich intronic or intergenic junk sequences that may play a role in chromosome structure and regulation.
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Affiliation(s)
- Lisa L Hall
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Cell & Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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