Nature Genetics, Journal Year: 2023, Volume and Issue: 55(8), P. 1359 - 1369
Published: July 3, 2023
Language: Английский
Nature Reviews Molecular Cell Biology, Journal Year: 2020, Volume and Issue: 21(8), P. 459 - 474
Published: April 20, 2020
Language: Английский
Citations
1017
Trends in Chemistry, Journal Year: 2019, Volume and Issue: 2(2), P. 123 - 136
Published: July 31, 2019
Endogenous DNA G-quadruplex (G4) structures have been detected in human cells and mapped genomic an endogenous chromatin context by adapting next-generation sequencing approaches, to reveal cell type- state-specific G4 landscapes a strong link of G4s with elevated transcription. Synthetic small molecules engineered antibodies vital probe existence functions cells.Several proteins found interact G4s, including helicases, transcription factors, epigenetic remodellers. Detailed structural functional studies provided novel insight into G4–protein interactions revealed potential involvement range biological processes.Multiple new lines evidence suggest that play role cancer growth progression. More are detectable states compared normal state, rendering highly interesting targets drug discovery. Recent started explore the for synthetic lethality global modulation gene Guanine-rich sequences can fold four-stranded, noncanonical secondary called G-quadruplexes (G4s). were initially considered curiosity, but recent suggests their key genome such as transcription, replication, stability, regulation, together numerous connections biology. Collectively, these advances stimulated research probing mechanisms consequent opportunities therapeutic intervention. Here, we provide perspective on structure function emphasis methodological enable study cells. We also critically examine mechanistic insights biology protein interaction partners highlight A chemist's molecule, or system molecules, is typically led consideration how molecular dictates function. The most widely recognised classical double helix [1Watson J.D. Crick F.H. Molecular nucleic acids; deoxyribose acid.Nature. 1953; 171: 737-738Crossref PubMed Scopus (6777) Google Scholar], which defines basis genetic code via defined base-pairing. Yet, it evident structurally dynamic capable adopting alternative structures. One class four-stranded (G4). Herein, discuss some scientific history has shaped our understanding this motif, its probable biology, major unanswered questions remain be solved. capacity guanylic acid derivatives self-aggregate was noted over century ago [2Bang I. Untersuchungen über die Guanylsäure.Biochem. Z. 1910; 26 (in German): 293-311Google Scholar]. Some 50 years later, fibre diffraction acids form right-handed helices leading proposed model strands stabilised Hoogsteen hydrogen-bonded guanines co-planar G-quartets [3Gellert M. et al.Helix formation acid.Proc. Natl. Acad. Sci. U. S. A. 1962; 48: 2013-2018Crossref Scholar, 4Arnott al.Structures polyinosinic polyguanylic acid.Biochem. 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Klug Telomeric dimerizes guanine tetrads between hairpin loops.Nature. 1989; 342: 825-829Crossref (702) Stacks cations centrally coordinated O6 stabilising preference monovalent order K+ > Na+ Li+ (Figure 1A ) [8Sen sodium-potassium switch G4-DNA.Nature. 1990; 344: 410-414Crossref (603) unimolecular intermolecular adopt wide diversity topologies arising different combinations strand direction 1D–F), well length loop composition [9Burge al.Quadruplex DNA: sequence, topology structure.Nucleic Acids Res. 2006; 34: 5402-5415Crossref (1328) 10Zhou al.Tri-G-quadruplex: controlled assembly three G-rich strands.Angew. Chemie Int. Ed. 2012; 51: 11002-11005Crossref (38) Structural X-ray crystallography NMR spectroscopy detailed primarily based telomeric repeat 1B,C) [11Parkinson G.N. al.Crystal quadruplexes DNA.Nature. 2002; 417: 876-880Crossref (1444) Scholar] derived promoter certain genes MYC KIT [12Ambrus al.Solution biologically relevant element c-MYC promoter. Implications stabilization.Biochemistry. 2005; 44: 2048-2058Crossref (352) 13Wei c-kit quadruplex reveals metal ions water maintaining conformation.Nucleic 40: 4691-4700Crossref (0) Based structures, algorithms sequence G≥3NxG≥3NxG≥3NxG≥3 developed deployed predict putative [14Huppert J.L. Balasubramanian Prevalence genome.Nucleic 33: 2908-2916Crossref (970) 15Todd A.K. al.Highly prevalent DNA.Nucleic 2901-2907Crossref (621) Early models assumed lengths no longer than seven requirement four continuous stretches Gs. Subsequently, several discontinuities G-stretches causing bulges observed [16Mukundan V.T. Phan A.T. Bulges G-quadruplexes: broadening definition G-quadruplex-forming sequences.J. Am. Chem. Soc. 2013; 135: 5017-5028Crossref (136) 17Sengar al.Structure (3+1) hybrid PARP1 promoter.Nucleic 2018; 47: 1564-1572Crossref (1) predictive [18Bedrat al.Re-evaluation propensity G4Hunter.Nucleic 2016; 1746-1759Crossref (138) availability large datasets enabled application machine learning forming [19Sahakyan A.B. al.Machine sequence-driven formation.Sci. Rep. 2017; 7: 1-11Crossref (12) Further considerations include effects crowding [20Shrestha P. al.Confined space facilitates formation.Nat. Nanotechnol. 12: 582-588Crossref (16) base modifications, cytosine methylation [21Hardin C.C. al.Cytosine—cytosine+ pairing stabilizes greatly enhances effect.Biochemistry. 1993; 32: 5870-5880Crossref oxidation [22Cheong V.V. al.Xanthine 8-oxoguanine G·G·X·O tetrad.Nucleic 2015; 43: 10506-10514PubMed stability Replicative immortality hallmark suggested achieve unlimited proliferation protecting ends chromosomes [23Hanahan Weinberg R.A. Hallmarks cancer: next generation.Cell. 2011; 144: 646-674Abstract Full Text PDF (26454) Telomerase reverse transcriptase enzyme adds segments 3′-end expressed cancers 24Testorelli C. cancer.J. Exp. Clin. Cancer 2003; 22: 165-169PubMed way inhibit action telomerase achieved sequester stable, liganded thought render inaccessible telomerase-mediated extension [25Sun al.Inhibition G-quadruplex-interactive compound.J. Med. 1997; 2113-2116Crossref An molecule daunomycin complex formed d(TGGGGT) confirmed stacking terminal G-quartet [26Clark G.R. first quadruplex-drug complex.J. 125: 4066-4067Crossref Several molecule-G4 since reported [27Neidle Quadruplex targets.J. 59: 5987-6011Crossref (179) concept targeting extended located promoters. cationic porphyrin TmPyP4, binds (but does bind duplex DNA) shown oncogene mechanism involve target nuclease hypersensitivity (NHE) [28Siddiqui-Jain al.Direct region repress transcription.Proc. 99: 11593-11598Crossref (1380) Since then, variety G4-targeted ligands described modulate expression carrying respective So far, few investigated transcriptional changes genome-wide level [29Marchetti al.Targeting multiple effector pathways pancreatic ductal adenocarcinoma G-quadruplex-binding molecule.J. 61: 2500-2517Crossref (19) carefully designed controls will needed assess whether particular fact main if result ligand binding other (G4 non-G4) targets. central hypothesis would strengthened more explicit actually engaging promoters affected cells, instance, employing methods mapping sites native [30Anders L. al.Genome-wide localization molecules.Nat. Biotechnol. 2014; 92-96Crossref (96) 31Tyler D.S. al.Click chemistry enables preclinical evaluation targeted therapies.Science. 356: 1401Crossref (31) To date, around 1000 G-Quadruplex Ligands Database (http://www.g4ldb.org/) [32Li Q. al.G4LDB: database discovering studying ligands.Nucleic 41: D1115-D1123Crossref examples used Figure 2B . Small binders generally aromatic surface π-π G-tetrads, positive charge basic groups loops grooves G4, steric bulk prevent intercalation double-stranded [33Monchaud Teulade-Fichou M.P. hitchhiker's guide ligands.Org. Biomol. 2008; 6: 627-636Crossref improve binding, ring count, charge, number hydrogen bond donors exceed what optimal good pharmacokinetic properties [34Ritchie T.J. Macdonald S.J.F. impact count compound developability - too many rings liability design?.Drug Discov. Today. 2009; 14: 1011-1020Crossref 35Shultz M.D. Two decades influence rule five changing approved oral drugs.J. 2019; 62: 1701-1714Crossref (13) Contrary perspective, noteworthy lacks traditional 'drug-like' significant accumulation efficacy tumour xenografts crystal MM41 bound 2A) features exploit additional groove [36Micco al.Structure-based design naphthalene diimide telomere agents cells.J. 56: 2959-2974Crossref (84) Interactions backbone phosphates do not require flat structure. Therefore, compounds reduced planarity (or high fsp3) and/or may merit G4s. Structure–activity relationship ligands, controlling physicochemical (fsp3), polarity (total polar area), lipophilicity (LogD), rotatable bonds optimum balance solubility, permeability. In structured RNA elements, previously realised increased strongly π-stacking leads off-target activity difficult further medicinal [37Warner K.D. al.Principles drug-like Rev. 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Many comprised loops, two G-tetrads caused discontinuous G-tracts organisms generate maps mammals (mouse, human), mostly absent studied [52Marsico al.Whole experimental species.Nucleic 1: 1-13Google It important consider all formation, unaccounted computational Efforts made landscape vivo. inferred immunoprecipitation high-throughput (ChIP-seq) experiments use against known 3C). 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Genet. 1267-1272Crossref (181) study, ∼10 uncovered precancerous while only ∼1000 'normal' counterpart NHEK represents 1% capability G4-Seq local majority nucleosome-depleted enriched regions. addition, particularly transcribed Mapping moderate overlap, indicating cell-type [60Hänsel-Hertsch sequencing.Nat. Protoc. 13: 551-564Crossref (4) antibody, D1, directly cervical carcinoma GFP-fusion protein. agreement signals start introns intergenic [44Liu Notably, ca. 15% exons, reflect specificities both differences landscapes, competition D1 G4-binding masked observation dependent regulated proteins. Indeed, natural Interacting Proteins Database, http://bsbe.iiti.ac.in/bsbe/ipdb/) [61Mishra S.K. al.G4IPDB: interacting proteins.Sci. 38144Crossref (21) identification relied proteomics oligomers baits isolate interactors extracts [62Cogoi al.Structural polymorphism within KRAS
Language: Английский
Citations
701
Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)
Published: June 23, 2021
Cell identity is maintained by activation of cell-specific gene programs, regulated epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma we confirmed that G4s promoters are invariably high levels open chromatin. Comparing G4 presence, location transcript available data keratinocytes, showed the same promoter sequences genes two cell lines had different G4-folding state: consistently G4-folding. Transcription AP-1 SP1, whose binding sites most significantly represented G4-folded sequences, coimmunoprecipitated their promoters. Thus, cooperate determine making strongly emerge as new regulators machinery.
Language: Английский
Citations
192
Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 48(1), P. 1 - 15
Published: Nov. 4, 2019
Abstract Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed characterization of specific G-quadruplex in vitro as well vivo, and at a much higher throughput, silico, which has greatly expanded our understanding G4-associated functions. Typically, consensus motif G3+N1–7G3+N1–7G3+N1–7G3+ been used to identify potential from primary sequence. Since, various algorithms developed predict formation quadruplexes directly sequences number studies reporting genome-wide G4 exploration across species rapidly increased. More recently, new methodologies also appeared, proposing other estimates consider non-canonical and/or structure propensity stability. The present review aims providing an updated overview current open-source prediction straightforward examples their implementation.
Language: Английский
Citations
189
Nature Genetics, Journal Year: 2020, Volume and Issue: 52(9), P. 878 - 883
Published: Aug. 3, 2020
Language: Английский
Citations
167
Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)
Published: July 22, 2019
Abstract Genome-wide studies of DNA replication origins revealed that preferentially associate with an Origin G-rich Repeated Element (OGRE), potentially forming G-quadruplexes (G4). Here, we functionally address their requirements for initiation in a series independent approaches. Deletion the OGRE/G4 sequence strongly decreased corresponding origin activity. Conversely, insertion element created new origin. This also promoted episomal EBV vectors lacking viral origin, but not if was deleted. A potent G4 ligand, PhenDC3, stabilized G4s did alter global However, set new, G4-associated created, whereas suppressed were largely G4-free. In vitro Xenopus laevis systems showed sequences are involved activation replication, pre-replication complex formation. Altogether, these results converge to functional importance elements initiation.
Language: Английский
Citations
156
Nucleic Acids Research, Journal Year: 2021, Volume and Issue: 50(3), P. e13 - e13
Published: Oct. 21, 2021
Abstract Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical affect gene expression, methylation, replication fork progression and genome stability. When how G4 are resolved remains unclear. Here we report the use of Cleavage Under Targets Tagmentation (CUT&Tag) for mapping native in mammalian cell lines at high resolution low background. Mild conditions used procedure retain more provide a higher signal-to-noise ratio than ChIP-based methods. We determine landscape mouse embryonic stem cells (ESC), observing widespread formation active promoters, poised enhancers. discover presence motifs distinguishes primed enhancers ESCs. Upon differentiation to neural progenitor (NPC), enhancer G4s lost. Further, performing R-loop CUT&Tag, demonstrate genome-wide co-occurrence single-stranded DNA, R loops promoters confirm exist independent ongoing transcription, suggesting an intricate relationship between transcription structures.
Language: Английский
Citations
139
Nature Chemistry, Journal Year: 2021, Volume and Issue: 13(7), P. 626 - 633
Published: June 28, 2021
Abstract DNA–protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential understand the underlying regulatory mechanisms on a molecular level. Here we describe co-binding-mediated protein profiling (CMPP) strategy investigate interactome of DNA G-quadruplexes (G4s) in native chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes endogenous G4s and subsequently crosslink co-binding G4-interacting situ. We first showed robustness by proximity labelling G4 binding vitro. Employing this approach live cells, then identified hundreds putative from various classes. Next, confirmed high G4-binding affinity selectivity for several newly discovered interactors vitro, validated direct functionally important candidate cellular chromatin using an independent approach. Our studies provide chemical map specific nucleic acid features living cells.
Language: Английский
Citations
121
Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)
Published: Jan. 10, 2022
Abstract The establishment of cell identity during embryonic development involves the activation specific gene expression programmes and is underpinned by epigenetic factors including DNA methylation histone post-translational modifications. G-quadruplexes are four-stranded secondary structures (G4s) that have been implicated in transcriptional regulation cancer. Here, we show G4s key genomic structural features linked to cellular differentiation. We find highly abundant human stem cells lost lineage specification. prevalent enhancers promoters. found common between downstream lineages tightly stabilisation genes involved essential functions as well transitions modification landscape. Furthermore, application small molecules stabilise causes a delay differentiation, keeping more pluripotent-like state. Collectively, our data highlight important coupled pluripotency
Language: Английский
Citations
75
Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(16), P. 8309 - 8321
Published: July 23, 2023
i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions vitro. Their formation cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed iMs within human genome live cells. mapped two cell lines recovered C-rich were confirmed to fold into found mainly present actively transcribing gene promoters, open chromatin regions, they overlap with R-loops, their abundance distribution specific each type. both long short C-tracts recovered, further extending relevance of iMs. By simultaneously mapping G-quadruplexes (G4s), which guanine-rich comparing results iMs, we proved can independent regions; however, when G4s same genomic tract, enhanced. genes low high transcription rates, respectively. Our findings support vivo iM provide new insights interplay as regulatory elements genome.
Language: Английский
Citations
52