51
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Carvalho ATP, Gouveia L, Kanna CR, Wärmländer SKTS, Platts JA, Kamerlin SCL. Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation. Epigenetics 2015; 9:1604-12. [PMID: 25625845 PMCID: PMC4622728 DOI: 10.4161/15592294.2014.988043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.
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Key Words
- AFM, Atomic Force Microscopy
- DDD, Dickerson-Drew Dodecamer
- DFT, Density Functional Theory
- DNA methylation
- DNA, Deoxyribonucleic Acid
- DNMT, DNA Methyltransferase
- LINEs, Long Interspred Transposable Elements
- MD, Molecular Dynamics
- MM, Molecular Mechanics
- MeCP, Methylated CpG-binding proteins
- PBC, Periodic Boundary Conditions
- QM, Quantum Mechanics
- RDF, Radial Distribution Functions
- RESP, Restrained Electrostatic Potentials Model
- SINEs, Short Interspred Transposable Elements
- SPME, Smooth Particle-Mesh Ewald
- TET, Translocation Proteins
- WT, Wild Type
- epigenetics
- indirect readout
- molecular dynamics
- recognition
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Affiliation(s)
- Alexandra T P Carvalho
- a Science for Life Laboratory; Department of Cell and Molecular Biology ; Uppsala University ; Uppsala , Sweden
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52
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Kubik G, Summerer D. Deciphering Epigenetic Cytosine Modifications by Direct Molecular Recognition. ACS Chem Biol 2015; 10:1580-9. [PMID: 25897631 DOI: 10.1021/acschembio.5b00158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Epigenetic modification at the 5-position of cytosine is a key regulatory element of mammalian gene expression with important roles in genome stability, development, and disease. The repertoire of cytosine modifications has long been confined to only 5-methylcytosine (mC) but has recently been expanded by the discovery of 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine. These are key intermediates of active mC demethylation but may additionally represent new epigenetic marks with distinct biological roles. This leap in chemical complexity of epigenetic cytosine modifications has not only created a pressing need for analytical approaches that enable unraveling of their functions, it has also created new challenges for such analyses with respect to sensitivity and selectivity. The crucial step of any such approach that defines its analytic potential is the strategy used for the actual differentiation of the cytosine 5-modifications from one another, and this selectivity can in principle be provided either by chemoselective conversions or by selective, molecular recognition events. While the former strategy has been particularly successful for accurate genomic profiling of cytosine modifications in vitro, the latter strategy provides interesting perspectives for simplified profiling of natural, untreated DNA, as well as for emerging applications such as single cell analysis and the monitoring of cytosine modification in vivo. We here review analytical techniques for the deciphering of epigenetic cytosine modifications with an emphasis on approaches that are based on the direct molecular recognition of these modifications in DNA.
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Affiliation(s)
- Grzegorz Kubik
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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53
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Szulik MW, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Correction to differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry 2015; 54:2550. [PMID: 25860080 PMCID: PMC4533905 DOI: 10.1021/acs.biochem.5b00344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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54
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Carvalho ATP, Gouveia ML, Raju Kanna C, Wärmländer SKTS, Platts J, Kamerlin SCL. Theoretical modelling of epigenetically modified DNA sequences. F1000Res 2015; 4:52. [PMID: 26448859 DOI: 10.12688/f1000research.6148.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2015] [Indexed: 11/20/2022] Open
Abstract
We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.
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Affiliation(s)
| | - Maria Leonor Gouveia
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, S-751 85, Sweden
| | - Charan Raju Kanna
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
| | | | - Jamie Platts
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
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55
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Carvalho ATP, Gouveia ML, Raju Kanna C, Wärmländer SKTS, Platts J, Kamerlin SCL. Theoretical modelling of epigenetically modified DNA sequences. F1000Res 2015; 4:52. [PMID: 26448859 PMCID: PMC4582758 DOI: 10.12688/f1000research.6148.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 12/20/2022] Open
Abstract
We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.
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Affiliation(s)
| | - Maria Leonor Gouveia
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, S-751 85, Sweden
| | - Charan Raju Kanna
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
| | | | - Jamie Platts
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-751 24, Sweden
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56
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Raiber EA, Murat P, Chirgadze DY, Beraldi D, Luisi BF, Balasubramanian S. 5-Formylcytosine alters the structure of the DNA double helix. Nat Struct Mol Biol 2015; 22:44-49. [PMID: 25504322 PMCID: PMC4287393 DOI: 10.1038/nsmb.2936] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/21/2014] [Indexed: 12/15/2022]
Abstract
The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-Å-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.
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Affiliation(s)
- Eun-Ang Raiber
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Dario Beraldi
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
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57
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Supek F, Lehner B, Hajkova P, Warnecke T. Hydroxymethylated cytosines are associated with elevated C to G transversion rates. PLoS Genet 2014; 10:e1004585. [PMID: 25211471 PMCID: PMC4161303 DOI: 10.1371/journal.pgen.1004585] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/07/2014] [Indexed: 11/23/2022] Open
Abstract
It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines. Most cytosines that occur in a CpG context in mammalian genomes are methylated. Methylation has important functional consequences in the cell but also affects genome evolution. Notably, methylated cytosines are prone to deaminate and constitute mutational hotspots in mammalian genomes. Recently, a series of other modifications, derived from the oxidation of methylated cytosines, was shown to exist in various mammalian cell types including embryonic stem cells. The most abundant of these modifications is 5-hydroxymethylcytosine. In this work, we ask whether methylated and hydroxymethylated cytosines are subject to the same mutational biases or lead to distinct patterns of genome evolution. To do so, we examine differences between individuals, between species, and between normal and cancer tissues alongside high-resolution maps of DNA methylation and hydroxymethylation in the human and mouse genomes. Unexpectedly, we find that hydroxymethylated cytosines are associated with more cytosine to guanine changes in both human and mouse populations, in closely related species, and in the context of somatic evolution in tumors. Based on multiple lines of evidence, we suggest that the different patterns of sequence evolution at methylated and hydroxymethylated sites are owing to differences in how these sites are handled by the DNA repair machinery.
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Affiliation(s)
- Fran Supek
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Ben Lehner
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain
| | - Petra Hajkova
- Reprogramming and Chromatin Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London, United Kingdom
| | - Tobias Warnecke
- Molecular Systems Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Campus, London, United Kingdom
- * E-mail:
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58
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Richa R, Sinha RP. Hydroxymethylation of DNA: an epigenetic marker. EXCLI JOURNAL 2014; 13:592-610. [PMID: 26417286 DOI: 10.17877/de290r-181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/08/2003] [Indexed: 05/25/2023]
Affiliation(s)
- Rajneesh Richa
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
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59
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Lercher L, McDonough MA, El-Sagheer AH, Thalhammer A, Kriaucionis S, Brown T, Schofield CJ. Structural insights into how 5-hydroxymethylation influences transcription factor binding. Chem Commun (Camb) 2013; 50:1794-6. [PMID: 24287551 DOI: 10.1039/c3cc48151d] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.
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Affiliation(s)
- Lukas Lercher
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, Oxford, UK.
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