1
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Kosel B, Bigler K, Buchmuller BC, Acharyya SR, Linser R, Summerer D. Evolved Readers of 5-Carboxylcytosine CpG Dyads Reveal a High Versatility of the Methyl-CpG-Binding Domain for Recognition of Noncanonical Epigenetic Marks. Angew Chem Int Ed Engl 2024; 63:e202318837. [PMID: 38284298 DOI: 10.1002/anie.202318837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Mammalian genomes are regulated by epigenetic cytosine (C) modifications in palindromic CpG dyads. Including canonical cytosine 5-methylation (mC), a total of four different 5-modifications can theoretically co-exist in the two strands of a CpG, giving rise to a complex array of combinatorial marks with unique regulatory potentials. While tailored readers for individual marks could serve as versatile tools to study their functions, it has been unclear whether a natural protein scaffold would allow selective recognition of marks that vastly differ from canonical, symmetrically methylated CpGs. We conduct directed evolution experiments to generate readers of 5-carboxylcytosine (caC) dyads based on the methyl-CpG-binding domain (MBD), the widely conserved natural reader of mC. Despite the stark steric and chemical differences to mC, we discover highly selective, low nanomolar binders of symmetric and asymmetric caC-dyads. Together with mutational and modelling studies, our findings reveal a striking evolutionary flexibility of the MBD scaffold, allowing it to completely abandon its conserved mC recognition mode in favour of noncanonical dyad recognition, highlighting its potential for epigenetic reader design.
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Affiliation(s)
- Brinja Kosel
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Katrin Bigler
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Benjamin C Buchmuller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Suchandra R Acharyya
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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2
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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3
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Bauer J, Reichl A, Tinnefeld P. Kinetic Referencing Allows Identification of Epigenetic Cytosine Modifications by Single-Molecule Hybridization Kinetics and Superresolution DNA-PAINT Microscopy. ACS NANO 2024; 18:1496-1503. [PMID: 38157484 DOI: 10.1021/acsnano.3c08451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We develop a DNA origami-based internal kinetic referencing system with a colocalized reference and target molecule to provide increased sensitivity and robustness for transient binding kinetics. To showcase this, we investigate the subtle changes in binding strength of DNA oligonucleotide hybrids induced by cytosine modifications. These cytosine modifications, especially 5-methylcytosine but also its oxidized derivatives, have been increasingly studied in the context of epigenetics. Recently revealed correlations of epigenetic modifications and disease also render them interesting biomarkers for early diagnosis. Internal kinetic referencing allows us to probe and compare the influence of the different epigenetic cytosine modifications on the strengths of 7-nucleotide long DNA hybrids with one or two modified nucleotides by single-molecule imaging of their transient binding, revealing subtle differences in binding times. Interestingly, the influence of epigenetic modifications depends on their position in the DNA strand, and in the case of two modifications, effects are additive. The sensitivity of the assay indicates its potential for the direct detection of epigenetic disease markers.
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Affiliation(s)
- Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Andreas Reichl
- Department of Chemistry, Ludwig-Maximilians-Universität München, Würmtalstraße 201, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
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4
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Symeonidis A, Chatzilygeroudi T, Chondrou V, Sgourou A. Contingent Synergistic Interactions between Non-Coding RNAs and DNA-Modifying Enzymes in Myelodysplastic Syndromes. Int J Mol Sci 2022; 23:ijms232416069. [PMID: 36555712 PMCID: PMC9785516 DOI: 10.3390/ijms232416069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell disorders with maturation and differentiation defects exhibiting morphological dysplasia in one or more hematopoietic cell lineages. They are associated with peripheral blood cytopenias and by increased risk for progression into acute myelogenous leukemia. Among their multifactorial pathogenesis, age-related epigenetic instability and the error-rate DNA methylation maintenance have been recognized as critical factors for both the initial steps of their pathogenesis and for disease progression. Although lower-risk MDS is associated with an inflammatory bone marrow microenvironment, higher-risk disease is delineated by immunosuppression and clonal expansion. "Epigenetics" is a multidimensional level of gene regulation that determines the specific gene networks expressed in tissues under physiological conditions and guides appropriate chromatin rearrangements upon influence of environmental stimulation. Regulation of this level consists of biochemical modifications in amino acid residues of the histone proteins' N-terminal tails and their concomitant effects on chromatin structure, DNA methylation patterns in CpG dinucleotides and the tissue-specific non-coding RNAs repertoire, which are directed against various gene targets. The role of epigenetic modifications is widely recognized as pivotal both in gene expression control and differential molecular response to drug therapies in humans. Insights to the potential of synergistic cooperations of epigenetic mechanisms provide new avenues for treatment development to comfort human diseases with a known epigenetic shift, such as MDS. Hypomethylating agents (HMAs), such as epigenetic modulating drugs, have been widely used in the past years as first line treatment for elderly higher-risk MDS patients; however, just half of them respond to therapy and are benefited. Rational outcome predictors following epigenetic therapy in MDS and biomarkers associated with disease relapse are of high importance to improve our efforts in developing patient-tailored clinical approaches.
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Affiliation(s)
- Argiris Symeonidis
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
- Medical School University of Patras, University Campus, 26500 Patras, Greece
| | - Theodora Chatzilygeroudi
- Hematology Division & Stem Cell Transplantation Unit, Department of Internal Medicine, University Hospital of Patras, 26504 Patras, Greece
| | - Vasiliki Chondrou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Argyro Sgourou
- Biology Laboratory, School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Correspondence:
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5
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Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovó P. 1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives. ACS PHYSICAL CHEMISTRY AU 2022; 2:237-246. [PMID: 35637781 PMCID: PMC9137243 DOI: 10.1021/acsphyschemau.1c00050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/29/2022]
Abstract
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5-Carboxycytosine
(5caC) is a rare epigenetic modification found
in nucleic acids of all domains of life. Despite its sparse genomic
abundance, 5caC is presumed to play essential regulatory roles in
transcription, maintenance and base-excision processes in DNA. In
this work, we utilize nuclear magnetic resonance (NMR) spectroscopy
to address the effects of 5caC incorporation into canonical DNA strands
at multiple pH and temperature conditions. Our results demonstrate
that 5caC has a pH-dependent global destabilizing and a base-pair
mobility enhancing local impact on dsDNA, albeit without any detectable
influence on the ground-state B-DNA structure. Measurement of hybridization
thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted
how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded
structure by ∼10–20 kJ mol–1 at 37
°C when compared to the same sample at neutral pH. Protonation
of 5caC results in a lower activation energy for the dissociation
process and a higher barrier for annealing. Studies on conformational
exchange on the microsecond time scale regime revealed a sharply localized
base-pair motion involving exclusively the modified site and its immediate
surroundings. By direct comparison with canonical and 5-formylcytosine
(5fC)-edited strands, we were able to address the impact of the two
most oxidized naturally occurring cytosine derivatives in the genome.
These insights on 5caC’s subtle sensitivity to acidic pH contribute
to the long-standing questions of its capacity as a substrate in base
excision repair processes and its purpose as an independent, stable
epigenetic mark.
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Affiliation(s)
- Romeo C. A. Dubini
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 5th floor, 80799 Munich, Germany
| | - Eva Korytiaková
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Thea Schinkel
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Pia Heinrichs
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Thomas Carell
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 5th floor, 80799 Munich, Germany
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
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6
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Jones EL, Mlotkowski AJ, Hebert SP, Schlegel HB, Chow CS. Calculations of p Ka Values for a Series of Naturally Occurring Modified Nucleobases. J Phys Chem A 2022; 126:1518-1529. [PMID: 35201779 DOI: 10.1021/acs.jpca.1c10905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its pKa value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the pKa values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the pKa values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the pKa values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.
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Affiliation(s)
- Evan L Jones
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Alan J Mlotkowski
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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7
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Tabatabaei SK, Pham B, Pan C, Liu J, Chandak S, Shorkey SA, Hernandez AG, Aksimentiev A, Chen M, Schroeder CM, Milenkovic O. Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing. NANO LETTERS 2022; 22:1905-1914. [PMID: 35212544 PMCID: PMC8915253 DOI: 10.1021/acs.nanolett.1c04203] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/22/2022] [Indexed: 05/23/2023]
Abstract
DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate single-molecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60% (39× larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.
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Affiliation(s)
- S Kasra Tabatabaei
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Bach Pham
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Chao Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Jingqian Liu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Shubham Chandak
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Spencer A Shorkey
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Charles M Schroeder
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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8
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Buchmuller BC, Dröden J, Singh H, Palei S, Drescher M, Linser R, Summerer D. Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads. J Am Chem Soc 2022; 144:2987-2993. [PMID: 35157801 PMCID: PMC8874921 DOI: 10.1021/jacs.1c10678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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5-Methylcytosine
(mC) and 5-hydroxymethylcytosine (hmC), the two
main epigenetic modifications of mammalian DNA, exist in symmetric
and asymmetric combinations in the two strands of CpG dyads. However,
revealing such combinations in single DNA duplexes is a significant
challenge. Here, we evolve methyl-CpG-binding domains (MBDs) derived
from MeCP2 by bacterial cell surface display, resulting in the first
affinity probes for hmC/mC CpGs. One mutant has low nanomolar affinity
for a single hmC/mC CpG, discriminates against all 14 other modified
CpG dyads, and rivals the selectivity of wild-type MeCP2. Structural
studies indicate that this protein has a conserved scaffold and recognizes
hmC and mC with two dedicated sets of residues. The mutant allows
us to selectively address and enrich hmC/mC-containing DNA fragments
from genomic DNA backgrounds. We anticipate that this novel probe
will be a versatile tool to unravel the function of hmC/mC marks in
diverse aspects of chromatin biology.
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Affiliation(s)
- Benjamin C Buchmuller
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Jessica Dröden
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Himanshu Singh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Shubhendu Palei
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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9
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Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms. Molecules 2021; 26:molecules26195728. [PMID: 34641273 PMCID: PMC8510025 DOI: 10.3390/molecules26195728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Thymine DNA Glycosylase (TDG) is an enzyme of the base excision repair mechanism and removes damaged or mispaired bases from DNA via hydrolysis of the glycosidic bond. Specificity is of high importance for such a glycosylase, so as to avoid the damage of intact DNA. Among the substrates reported for TDG are mispaired uracil and thymine but also formyl-cytosine and carboxyl-cytosine. Methyl-cytosine and hydroxylmethyl-cytosine are, in contrast, not processed by the TDG enzyme. We have in this work employed molecular dynamics simulations to explore the conformational dynamics of DNA carrying a formyl-cytosine or carboxyl-cytosine and compared those to DNA with the non-cognate bases methyl-cytosine and hydroxylmethyl-cytosine, as amino and imino tautomers. Whereas for the mispairs a wobble conformation is likely decisive for recognition, all amino tautomers of formyl-cytosine and carboxyl-cytosine exhibit the same Watson–Crick conformation, but all imino tautomers indeed form wobble pairs. The conformational dynamics of the amino tautomers in free DNA do not exhibit differences that could be exploited for recognition, and also complexation to the TDG enzyme does not induce any alteration that would indicate preferable binding to one or the other oxidised methyl-cytosine. The imino tautomers, in contrast, undergo a shift in the equilibrium between a closed and a more open, partially flipped state, towards the more open form upon complexation to the TDG enzyme. This stabilisation of the more open conformation is most pronounced for the non-cognate bases methyl-cytosine and hydroxyl-cytosine and is thus not a likely mode for recognition. Moreover, calculated binding affinities for the different forms indicate the imino forms to be less likely in the complexed DNA. These findings, together with the low probability of imino tautomers in free DNA and the indifference of the complexed amino tautomers, suggest that discrimination of the oxidised methyl-cytosines does not take place in the initial complex formation.
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10
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Wong KL, Liu J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol J 2021; 16:e2000338. [PMID: 34411451 DOI: 10.1002/biot.202000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.
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Affiliation(s)
- Kingsley L Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
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11
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Furukawa A, Walinda E, Arita K, Sugase K. Structural dynamics of double-stranded DNA with epigenome modification. Nucleic Acids Res 2021; 49:1152-1162. [PMID: 33337470 PMCID: PMC7826269 DOI: 10.1093/nar/gkaa1210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/15/2022] Open
Abstract
Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of DNA is known to affect the binding of proteins to methylated DNA. Here, we have carried out a semi-quantitative analysis of the dynamics of double-stranded DNA (dsDNA) containing various epigenetic modifications by combining data from imino 1H exchange and imino 1H R1ρ relaxation dispersion NMR experiments in a complementary way. Using this approach, we characterized the base-opening (kopen) and base-closing (kclose) rates, facilitating a comparison of the base-opening and -closing process of dsDNA containing cytosine in different states of epigenetic modification. A particularly striking result is the increase in the kopen rate of hemi-methylated dsDNA 5mC/C relative to unmodified or fully methylated dsDNA, indicating that the Watson-Crick base pairs undergo selective destabilization in 5mC/C. Collectively, our findings imply that the epigenetic modulation of cytosine dynamics in dsDNA mediates destabilization of the GC Watson-Crick base pair to allow base-flipping in living cells.
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Affiliation(s)
- Ayako Furukawa
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika, Soraku, Kyoto 619-0284, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika, Soraku, Kyoto 619-0284, Japan
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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12
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Tsuruta M, Sugitani Y, Sugimoto N, Miyoshi D. Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes. Int J Mol Sci 2021; 22:ijms22020947. [PMID: 33477917 PMCID: PMC7833394 DOI: 10.3390/ijms22020947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/31/2022] Open
Abstract
Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.
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Affiliation(s)
- Mitsuki Tsuruta
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Yui Sugitani
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Correspondence: ; Tel.: +81-(07)-8303-1426
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13
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de Oliveira DT, Guerra-Sá R. Uncovering epigenetic landscape: a new path for biomarkers identification and drug development. Mol Biol Rep 2020; 47:9097-9122. [PMID: 33089404 DOI: 10.1007/s11033-020-05916-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022]
Abstract
Scientific advances in recent decades have revealed an incredible degree of plasticity in gene expression in response to various environmental, nutritional, physiological, pathological, and behavioral conditions. Epigenetics emerges in this sense, as the link between the internal (genetic) and external (environmental) factors underlying the expression of the phenotype. Methylation of DNA and histone post-translationa modifications are canonical epigenetic events. Additionally, noncoding RNAs molecules (microRNAs and lncRNAs) have also been proposed as another layer of epigenetic regulation. Together, these events are responsible for regulating gene expression throughout life, controlling cellular fate in both normal and pathological development. Despite being a relatively recent science, epigenetics has been arousing the interest of researchers from different segments of the life sciences and the general public. This review highlights the recent advances in the characterization of the epigenetic events and points promising use of these brands for the diagnosis, prognosis, and therapy of diseases. We also present several classes of epigenetic modifying compounds with therapeutic applications (so-call epidrugs) and their current status in clinical trials and approved by the FDA. In summary, hopefully, we provide the reader with theoretical bases for a better understanding of the epigenetic mechanisms and of the promising application of these marks and events in the medical clinic.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Renata Guerra-Sá
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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14
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Ray S, Tillo D, Ufot A, Assad N, Durell S, Vinson C. bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine. Biochemistry 2020; 59:3529-3540. [PMID: 32902247 DOI: 10.1021/acs.biochem.0c00475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mammalian cells, 5-methylcytosine (5mC) occurs in genomic double-stranded DNA (dsDNA) and is enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), then to 5-formylcytosine (5fC), and finally to 5-carboxylcytosine (5caC). These cytosine modifications are enriched in regulatory regions of the genome. The effect of these oxidative products on five bZIP dimers (CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun) binding to five types of dsDNA was measured using protein binding microarrays. The five dsDNAs contain either cytosine in both DNA strands or cytosine in one strand and either 5mC, 5hmC, 5fC, or 5caC in the second strand. Some sequences containing the CEBP half-site GCAA are bound more strongly by all five bZIP domains when dsDNA contains 5mC, 5hmC, or 5fC. dsDNA containing 5caC in some TRE (AP-1)-like sequences, e.g., TGACTAA, is better bound by Zta, ATF3|cJun, and cFos|cJun.
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15
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Dubini RCA, Schön A, Müller M, Carell T, Rovó P. Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange. Nucleic Acids Res 2020; 48:8796-8807. [PMID: 32652019 PMCID: PMC7470965 DOI: 10.1093/nar/gkaa589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/24/2020] [Accepted: 07/02/2020] [Indexed: 12/23/2022] Open
Abstract
5-Formylcytosine (5fC) is a chemically edited, naturally occurring nucleobase which appears in the context of modified DNA strands. The understanding of the impact of 5fC on dsDNA physical properties is to date limited. In this work, we applied temperature-dependent 1H Chemical Exchange Saturation Transfer (CEST) NMR experiments to non-invasively and site-specifically measure the thermodynamic and kinetic influence of formylated cytosine nucleobase on the melting process involving dsDNA. Incorporation of 5fC within symmetrically positioned CpG sites destabilizes the whole dsDNA structure-as witnessed from the ∼2°C decrease in the melting temperature and 5-10 kJ mol-1 decrease in ΔG°-and affects the kinetic rates of association and dissociation. We observed an up to ∼5-fold enhancement of the dsDNA dissociation and an up to ∼3-fold reduction in ssDNA association rate constants, over multiple temperatures and for several proton reporters. Eyring and van't Hoff analysis proved that the destabilization is not localized, instead all base-pairs are affected and the transition states resembles the single-stranded conformation. These results advance our knowledge about the role of 5fC as a semi-permanent epigenetic modification and assist in the understanding of its interactions with reader proteins.
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Affiliation(s)
- Romeo C A Dubini
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799 Munich, Germany
| | - Alexander Schön
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Markus Müller
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Thomas Carell
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377 Munich, Germany
- Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799 Munich, Germany
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16
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Pol β gap filling, DNA ligation and substrate-product channeling during base excision repair opposite oxidized 5-methylcytosine modifications. DNA Repair (Amst) 2020; 95:102945. [PMID: 32853828 DOI: 10.1016/j.dnarep.2020.102945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/07/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation on cytosine in CpG islands generates 5-methylcytosine (5mC), and further modification of 5mC can result in the oxidized variants 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxy (5caC). Base excision repair (BER) is crucial for both genome maintenance and active DNA demethylation of modified cytosine products and involves substrate-product channeling from nucleotide insertion by DNA polymerase (pol) β to the subsequent ligation step. Here, we report that, in contrast to the pol β mismatch insertion products (dCTP, dATP, and dTTP), the nicked products after pol β dGTP insertion can be ligated by DNA ligase I or DNA ligase III/XRCC1 complex when a 5mC oxidation modification is present opposite in the template position in vitro. A Pol β K280A mutation, which perturbates the stabilization of these base modifications within the active site, hinders the BER ligases. Moreover, the nicked repair intermediates that mimic pol β mismatch insertion products, i.e., with 3'-preinserted dGMP or dTMP opposite templating 5hmC, 5fC or 5caC, can be efficiently ligated, whereas preinserted 3'-dAMP or dCMP mismatches result in failed ligation reactions. These findings herein contribute to our understanding of the insertion tendencies of pol β opposite different cytosine base forms, the ligation properties of DNA ligase I and DNA ligase III/XRCC1 complex in the context of gapped and nicked damage-containing repair intermediates, and the efficiency and fidelity of substrate channeling during the final steps of BER in situations involving oxidative 5mC base modifications in the template strand.
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17
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Vongsutilers V, Shinohara Y, Kawai G. Epigenetic TET-Catalyzed Oxidative Products of 5-Methylcytosine Impede Z-DNA Formation of CG Decamers. ACS OMEGA 2020; 5:8056-8064. [PMID: 32309715 PMCID: PMC7161056 DOI: 10.1021/acsomega.0c00120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/19/2020] [Indexed: 05/12/2023]
Abstract
Methylation of cytosine has been known to play a significant role in epigenetic regulation. 5-Methylcytosine was among the first base modification that was discovered for the capability to facilitate B/Z-DNA transition as observed in CG repeated tracks. A study on gene repression by Z-DNA prone sequence as in ADAM-12 has ignited our research interest for the Z-DNA role in epigenetics. Ten eleven translocation family proteins are responsible to catalyze 5-methylcytosine to produce oxidative products including 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine, which each may have unique function rather than the sole purpose of 5-methylcytosine clearance. Although the Z-DNA-promoting effect of 5-methylcytosine was well established, the effect of its oxidative products on Z-DNA remain unknown. In this study, the Z-DNA-promoting effect of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine on the CG decamer model were investigated along with known Z-DNA stabilizers, 5-methylcytosine and 8-oxoguanine. Experimental results from circular dichroism (CD) and NMR indicates that all oxidative products of 5-methylcytosine hinder B/Z-DNA transition as high salt concentration suitable to stabilize and convert unmodified CG decamer to Z-DNA conformation is insufficient to facilitate the B/Z-DNA transition of CG decamer containing 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxycytosine. Molecular dynamic simulation and free energy calculation by MM-PBSA are in agreement with the experimental finding that 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine destabilize Z-DNA conformation of CG decamer, in contrast to its precursor. Investigation of Z-DNA switch-on/switch-off regulated by 5-methylcytosine and its oxidative products is a further step to elucidate the potential of epigenetic regulated via Z-DNA.
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Affiliation(s)
- Vorasit Vongsutilers
- Department
of Food and Pharmaceutical Chemistry, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Yoko Shinohara
- Department
of Life and Environmental Sciences, Chiba
Institute of Technology, Chiba 275-0016, Japan
| | - Gota Kawai
- Department
of Life and Environmental Sciences, Chiba
Institute of Technology, Chiba 275-0016, Japan
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18
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Schneider M, Trummer C, Stengl A, Zhang P, Szwagierczak A, Cardoso MC, Leonhardt H, Bauer C, Antes I. Systematic analysis of the binding behaviour of UHRF1 towards different methyl- and carboxylcytosine modification patterns at CpG dyads. PLoS One 2020; 15:e0229144. [PMID: 32084194 PMCID: PMC7034832 DOI: 10.1371/journal.pone.0229144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/30/2020] [Indexed: 01/24/2023] Open
Abstract
The multi-domain protein UHRF1 is essential for DNA methylation maintenance and binds DNA via a base-flipping mechanism with a preference for hemi-methylated CpG sites. We investigated its binding to hemi- and symmetrically modified DNA containing either 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), or 5-carboxylcytosine (caC). Our experimental results indicate that UHRF1 binds symmetrically carboxylated and hybrid methylated/carboxylated CpG dyads in addition to its previously reported substrates. Complementary molecular dynamics simulations provide a possible mechanistic explanation of how the protein could differentiate between modification patterns. First, we observe different local binding modes in the nucleotide binding pocket as well as the protein's NKR finger. Second, both DNA modification sites are coupled through key residues within the NKR finger, suggesting a communication pathway affecting protein-DNA binding for carboxylcytosine modifications. Our results suggest a possible additional function of the hemi-methylation reader UHRF1 through binding of carboxylated CpG sites. This opens the possibility of new biological roles of UHRF1 beyond DNA methylation maintenance and of oxidised methylcytosine derivates in epigenetic regulation.
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Affiliation(s)
- Markus Schneider
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Carina Trummer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Andreas Stengl
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Peng Zhang
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Aleksandra Szwagierczak
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics at the Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Christina Bauer
- Center for Integrated Protein Science Munich at the Department of Biology II, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the TUM School of Life Sciences, Technische Universität München, Freising, Germany
- * E-mail:
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19
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Sanstead PJ, Ashwood B, Dai Q, He C, Tokmakoff A. Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA. J Phys Chem B 2020; 124:1160-1174. [PMID: 31986043 PMCID: PMC7136776 DOI: 10.1021/acs.jpcb.9b11511] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The naturally occurring nucleobase 5-methylcytosine (mC) and its oxidized derivatives 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC) play important roles in epigenetic regulation and, along with cytosine (C), represent nucleobases currently implicated in the active cytosine demethylation pathway. Despite considerable interest in these modified bases, their impact on the thermodynamic stability of double-stranded DNA (dsDNA) remains ambiguous and their influence on hybridization kinetics and dynamics is even less well-understood. To address these unknowns, we employ steady-state and time-resolved infrared spectroscopy to measure the influence of cytosine modification on the thermodynamics and kinetics of hybridization by assessing the impact on local base pairing dynamics, shifts in the stability of the duplex state, and changes to the hybridization transition state. Modification with mC leads to more tightly bound base pairing below the melting transition and stabilizes the duplex relative to canonical DNA, but the free energy barrier to dehybridization at physiological temperature is nevertheless reduced slightly. Both hmC and fC lead to an increase in local base pair fluctuations, a reduction in the cooperativity of duplex melting, and a lowering of the dissociation barrier, but these effects are most pronounced when the 5-position is formylated. The caC nucleobase demonstrates little impact on dsDNA under neutral conditions, but we find that this modification can dynamically switch between C-like and fC-like behavior depending on the protonation state of the 5-position carboxyl group. Our results provide a consistent thermodynamic and kinetic framework with which to describe the modulation of the physical properties of double-stranded DNA containing these modified nucleobases.
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Affiliation(s)
- Paul J. Sanstead
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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20
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Ashwood B, Sanstead PJ, Dai Q, He C, Tokmakoff A. 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex. J Phys Chem B 2020; 124:627-640. [PMID: 31873021 DOI: 10.1021/acs.jpcb.9b11510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Applications associated with nucleobase protonation events are grounded in their fundamental impact on DNA thermodynamics, structure, and hybridization dynamics. Of the canonical nucleobases, N3 protonation of cytosine (C) is the most widely utilized in both biology and nanotechnology. Naturally occurring C derivatives that shift the N3 pKa introduce an additional level of tunability. The epigenetic nucleobase 5-carboxylcytosine (caC) presents a particularly interesting example since this derivative forms Watson-Crick base pairs of similar stability and displays pH-dependent behavior over the same range as the canonical nucleobase. However, the titratable group in caC corresponds to the exocyclic carboxyl group rather than N3, and the implications of these divergent protonation events toward DNA hybridization thermodynamics, kinetics, and base pairing dynamics remain poorly understood. Here, we study the pH dependence of these physical properties using model oligonucleotides containing C and caC with FTIR and temperature-jump IR spectroscopy. We demonstrate that N3 protonation of C completely disrupts duplex stability, leading to large shifts in the duplex/single-strand equilibrium, a reduction in the cooperativity of melting, and an acceleration in the rate of duplex dissociation. In contrast, while increasing 5-carboxyl protonation in caC-containing duplexes induces an increase in base pair fluctuations, the DNA duplex can tolerate substantial protonation without significant perturbation to the duplex/single-strand equilibrium. However, 5-carboxyl protonation has a large impact on hybridization kinetics by reducing the transition state free energy. Our thermodynamic and kinetic analysis provides new insight on the impact of two divergent protonation mechanisms in naturally occurring nucleobases on the biophysical properties of DNA.
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21
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DNA Modification Readers and Writers and Their Interplay. J Mol Biol 2019:S0022-2836(19)30718-1. [PMID: 31866298 DOI: 10.1016/j.jmb.2019.12.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Genomic DNA is modified in a postreplicative manner and several modifications, the enzymes responsible for their deposition as well as proteins that read these modifications, have been described. Here, we focus on the impact of DNA modifications on the DNA helix and review the writers and readers of cytosine modifications and how they interplay to shape genome composition, stability, and function.
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22
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Yang J, Zhang X, Blumenthal RM, Cheng X. Detection of DNA Modifications by Sequence-Specific Transcription Factors. J Mol Biol 2019:S0022-2836(19)30568-6. [PMID: 31626807 DOI: 10.1016/j.jmb.2019.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
The establishment, detection, and alteration or elimination of epigenetic DNA modifications are essential to controlling gene expression ranging from bacteria to mammals. The DNA methylations occurring at cytosine and adenine are carried out by SAM-dependent methyltransferases. Successive oxidations of 5-methylcytosine (5mC) by Tet dioxygenases generate 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) derivatives; thus, DNA elements with multiple methylation sites can have a wide range of modification states. In contrast, oxidation of N6-methyladenine by homologs of Escherichia coli AlkB removes the methyl group directly. Both Tet and AlkB enzymes are 2-oxoglutarate- and Fe(II)-dependent dioxygenases. DNA-binding proteins decode the modification status of specific genomic regions. This article centers on two families of sequence-specific transcription factors: bZIP (basic leucine-zipper) proteins, exemplified by the AP-1 and CEBPβ recognition of 5mC; and bHLH (basic helix-loop-helix) proteins, exemplified by MAX and TCF4 recognition of 5caC. We discuss the impact of template strand DNA modification on the activities of DNA and RNA polymerases, and the varied tendencies of modifications to alter base pairing and their interactions with DNA repair enzymes.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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23
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Nanan KK, Sturgill DM, Prigge MF, Thenoz M, Dillman AA, Mandler MD, Oberdoerffer S. TET-Catalyzed 5-Carboxylcytosine Promotes CTCF Binding to Suboptimal Sequences Genome-wide. iScience 2019; 19:326-339. [PMID: 31404833 PMCID: PMC6699469 DOI: 10.1016/j.isci.2019.07.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
The mechanisms supporting dynamic regulation of CTCF-binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC), as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ~13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.
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Affiliation(s)
- Kyster K Nanan
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria F Prigge
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan Thenoz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allissa A Dillman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Deckard CE, Banerjee DR, Sczepanski JT. Chromatin Structure and the Pioneering Transcription Factor FOXA1 Regulate TDG-Mediated Removal of 5-Formylcytosine from DNA. J Am Chem Soc 2019; 141:14110-14114. [PMID: 31460763 DOI: 10.1021/jacs.9b07576] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although a functional relationship between active DNA demethylation and chromatin structure is often implied, direct experimental evidence is lacking. We investigated the relationship between chromatin structure and thymine DNA glycosylase (TDG) using chemically defined nucleosome arrays containing site-specifically positioned 5-formylcytosine (5fC) residues. We show that the extent of array compaction, as well as nucleosome positioning, dramatically influence the ability of TDG to excise 5fC from DNA, indicating that the chromatin structure is likely a key determinant of whether 5fC is removed from the genome or retained as an epigenetic mark. Furthermore, the H2A.Z/H3.3 double-variant nucleosome and the pioneering transcription factor forkhead box A1 (FOXA1), both of which are implicated in shaping the chromatin landscape during demethylation of tissue-specific enhancers, differentially regulate TDG activity on chromatin. Together, this work provides the first direct evidence that the higher order chromatin structure regulates active DNA demethylation through TDG and provides novel insights into the mechanism of 5fC turnover at enhancers.
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Affiliation(s)
- Charles E Deckard
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Deb Ranjan Banerjee
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Jonathan T Sczepanski
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
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Abstract
5-Formyl-2'-deoxycytidine (5fdC) is a naturally occurring nucleobase that is broadly distributed in genomic DNA. 5fdC is produced via the oxidation of 5-methylcytosine (5mdC) by ten-eleven translocation enzyme (TET) and can be further converted to 5-carboxylcytosine (5cadC) by TET. Both 5fdC and 5cadC can be restored to dC by TDG-mediated base excision repair and direct deformylation/decarboxylation. Thus, 5fdC is considered an intermediate in the TET-mediated DNA demethylation pathway. 5fdC also alters the structure and stability of genomic DNA and affects genetic expression. This review summarizes the recent research on 5fdC, detailing its formation, detection and distribution, biological functions and transformation in cells. The challenges and future prospects to further explore the function and metabolism of 5fdC are briefly discussed at the end.
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Affiliation(s)
- Yingqian Zhang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.
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Rathi P, Maurer S, Summerer D. Selective recognition of N4-methylcytosine in DNA by engineered transcription-activator-like effectors. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0078. [PMID: 29685980 DOI: 10.1098/rstb.2017.0078] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2017] [Indexed: 01/03/2023] Open
Abstract
The epigenetic DNA nucleobases 5-methylcytosine (5mC) and N4-methylcytosine (4mC) coexist in bacterial genomes and have important functions in host defence and transcription regulation. To better understand the individual biological roles of both methylated nucleobases, analytical strategies for distinguishing unmodified cytosine (C) from 4mC and 5mC are required. Transcription-activator-like effectors (TALEs) are programmable DNA-binding repeat proteins, which can be re-engineered for the direct detection of epigenetic nucleobases in user-defined DNA sequences. We here report the natural, cytosine-binding TALE repeat to not strongly differentiate between 5mC and 4mC. To engineer repeats with selectivity in the context of C, 5mC and 4mC, we developed a homogeneous fluorescence assay and screened a library of size-reduced TALE repeats for binding to all three nucleobases. This provided insights into the requirements of size-reduced TALE repeats for 4mC binding and revealed a single mutant repeat as a selective binder of 4mC. Employment of a TALE with this repeat in affinity enrichment enabled the isolation of a user-defined DNA sequence containing a single 4mC but not C or 5mC from the background of a bacterial genome. Comparative enrichments with TALEs bearing this or the natural C-binding repeat provides an approach for the complete, programmable decoding of all cytosine nucleobases found in bacterial genomes.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Preeti Rathi
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Sara Maurer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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27
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Howard MJ, Foley KG, Shock DD, Batra VK, Wilson SH. Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase β. J Biol Chem 2019; 294:7194-7201. [PMID: 30885943 DOI: 10.1074/jbc.ra118.006809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/13/2019] [Indexed: 01/10/2023] Open
Abstract
DNA methylation is an epigenetic mark that regulates gene expression in mammals. One method of methylation removal is through ten-eleven translocation-catalyzed oxidation and the base excision repair pathway. The iterative oxidation of 5-methylcytosine catalyzed by ten-eleven translocation enzymes produces three oxidized forms of cytosine: 5-hydroxmethylcytosine, 5-formylcytosine, and 5-carboxycytosine. The effect these modifications have on the efficiency and fidelity of the base excision repair pathway during the repair of opposing base damage, and in particular DNA polymerization, remains to be elucidated. Using kinetic assays, we show that the catalytic efficiency for the incorporation of dGTP catalyzed by human DNA polymerase β is not affected when 5-methylcytosine, 5-hydroxmethylcytosine, and 5-formylcytosine are in the DNA template. In contrast, the catalytic efficiency of dGTP insertion decreases ∼20-fold when 5-carboxycytosine is in the templating position, as compared with unmodified cytosine. However, DNA polymerase fidelity is unaltered when these modifications are in the templating position. Structural analysis reveals that the methyl, hydroxymethyl, and formyl modifications are easily accommodated within the polymerase active site. However, to accommodate the carboxyl modification, the phosphate backbone on the templating nucleotide shifts ∼2.5 Å to avoid a potential steric/repulsive clash. This altered conformation is stabilized by lysine 280, which makes a direct interaction with the carboxyl modification and the phosphate backbone of the templating strand. This work provides the molecular basis for the accommodation of epigenetic base modifications in a polymerase active site and suggests that these modifications are not mutagenically copied during base excision repair.
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Affiliation(s)
- Michael J Howard
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - K Grace Foley
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - David D Shock
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Vinod K Batra
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Samuel H Wilson
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Zagorskaitė E, Manakova E, Sasnauskas G. Recognition of modified cytosine variants by the DNA-binding domain of methyl-directed endonuclease McrBC. FEBS Lett 2018; 592:3335-3345. [PMID: 30194838 DOI: 10.1002/1873-3468.13244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/10/2018] [Accepted: 09/05/2018] [Indexed: 01/21/2023]
Abstract
Cytosine modifications expand the information content of genomic DNA in both eukaryotes and prokaryotes, providing means for epigenetic regulation and self versus nonself discrimination. For example, the methyl-directed restriction endonuclease, McrBC, recognizes and cuts invading bacteriophage DNA containing 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N4-methylcytosine (4mC), leaving the unmodified host DNA intact. Here, we present cocrystal structures of McrB-N bound to DNA oligoduplexes containing 5hmC, 5-formylcytosine (5fC), and 4mC, and characterize the relative affinity of McrB-N to various cytosine variants. We find that McrB-N flips out modified bases into a protein pocket and binds cytosine derivatives in the order of descending affinity: 4mC > 5mC > 5hmC ≫ 5fC. We also show that pocket mutations alter the relative preference of McrB-N to 5mC, 5hmC, and 4mC.
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Affiliation(s)
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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30
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Maurer S, Buchmuller B, Ehrt C, Jasper J, Koch O, Summerer D. Overcoming conservation in TALE-DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-methylcytosine. Chem Sci 2018; 9:7247-7252. [PMID: 30288245 PMCID: PMC6148557 DOI: 10.1039/c8sc01958d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Transcription-activator-like effectors (TALEs) are repeat-based proteins featuring programmable DNA binding. The repulsion of TALE repeats by 5-methylcytosine (5mC) and its oxidized forms makes TALEs potential probes for their programmable analysis. However, this potential has been limited by the inability to engineer repeats capable of actual, fully selective binding of an (oxidized) 5mC: the extremely conserved and simple nucleobase recognition mode of TALE repeats and their extensive involvement in inter-repeat interactions that stabilize the TALE fold represent major engineering hurdles. We evaluated libraries of alternative, strongly truncated repeat scaffolds and discovered a repeat that selectively recognizes 5-carboxylcytosine (5caC), enabling construction of the first programmable receptors for an oxidized 5mC. In computational studies, this unusual scaffold executes a dual function via a critical arginine that provides inter-repeat stabilization and selectively interacts with the 5caC carboxyl group via a salt-bridge. These findings argue for an unexpected adaptability of TALE repeats and provide a new impulse for the design of programmable probes for nucleobases beyond A, G, T and C.
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Affiliation(s)
- Sara Maurer
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
| | - Benjamin Buchmuller
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
| | - Julia Jasper
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn Str. 4a , 44227 Dortmund , Germany .
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31
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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32
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018. [DOI: https://doi.org/10.1155/2018/8764384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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33
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Dietzsch J, Feineis D, Höbartner C. Chemoselective labeling and site-specific mapping of 5-formylcytosine as a cellular nucleic acid modification. FEBS Lett 2018; 592:2032-2047. [DOI: 10.1002/1873-3468.13058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Julia Dietzsch
- Institute of Organic Chemistry; University of Würzburg; Germany
| | - Doris Feineis
- Institute of Organic Chemistry; University of Würzburg; Germany
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34
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Gieß M, Witte A, Jasper J, Koch O, Summerer D. Complete, Programmable Decoding of Oxidized 5-Methylcytosine Nucleobases in DNA by Chemoselective Blockage of Universal Transcription-Activator-Like Effector Repeats. J Am Chem Soc 2018; 140:5904-5908. [DOI: 10.1021/jacs.8b02909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Mario Gieß
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Anna Witte
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Julia Jasper
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Oliver Koch
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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35
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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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36
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Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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37
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Schneider B, Božíková P, Nečasová I, Čech P, Svozil D, Černý J. A DNA structural alphabet provides new insight into DNA flexibility. Acta Crystallogr D Struct Biol 2018; 74:52-64. [PMID: 29372899 PMCID: PMC5786007 DOI: 10.1107/s2059798318000050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/02/2018] [Indexed: 11/10/2022] Open
Abstract
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Iva Nečasová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018; 2018:8764384. [PMID: 30073137 PMCID: PMC6057397 DOI: 10.1155/2018/8764384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 02/05/2023] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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39
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Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD. Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem Res Toxicol 2017; 30:1993-2001. [PMID: 28862449 PMCID: PMC6494084 DOI: 10.1021/acs.chemrestox.7b00173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways. In some cases, the altered base acts as a mutagen, altering the DNA sequence to promote cellular death; in others, insertion of the altered nucleotide triggers DNA repair pathways, which produce lethal levels of cytotoxic intermediates such as single and double stranded DNA breaks. As a prerequisite to many of these biological outcomes, the modified nucleotide must be accommodated in the DNA polymerase active site during nucleotide insertion. Currently, the molecular contacts that mediate DNA polymerase insertion of modified nucleotides remain unknown for multiple therapeutic compounds, despite decades of clinical use. To determine how modified bases are inserted into duplex DNA, we used mammalian DNA polymerase β (pol β) to visualize the structural conformations of four therapeutically relevant modified nucleotides, 6-thio-2'-deoxyguanosine-5'-triphosphate (6-TdGTP), 5-fluoro-2'-deoxyuridine-5'-triphosphate (5-FdUTP), 5-formyl-deoxycytosine-5'-triphosphate (5-FodCTP), and 5-formyl-deoxyuridine-5'-triphosphate (5-FodUTP). Together, the structures reveal a pattern in which the modified nucleotides utilize Watson-Crick base pairing interactions similar to that of unmodified nucleotides. The nucleotide modifications were consistently positioned in the major groove of duplex DNA, accommodated by an open cavity in pol β. These results provide novel information for the rational design of new therapeutic nucleoside analogues and a greater understanding of how modified nucleotides are tolerated by polymerases.
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Affiliation(s)
| | | | | | | | - Bret D. Freudenthal
- Corresponding Author 4015 Wahl Hall West, Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center Kansas City, Kansas 66160. Phone: 913-588-5560,
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40
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Rathi P, Witte A, Summerer D. Engineering DNA Backbone Interactions Results in TALE Scaffolds with Enhanced 5-Methylcytosine Selectivity. Sci Rep 2017; 7:15067. [PMID: 29118409 PMCID: PMC5678105 DOI: 10.1038/s41598-017-15361-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are DNA major-groove binding proteins widely used for genome targeting. TALEs contain an N-terminal region (NTR) and a central repeat domain (CRD). Repeats of the CRD selectively recognize each one DNA nucleobase, offering programmability. Moreover, repeats with selectivity for 5-methylcytosine (5mC) and its oxidized derivatives can be designed for analytical applications. However, both TALE domains also nonspecifically interact with DNA phosphates via basic amino acids. To enhance the 5mC selectivity of TALEs, we aimed to decrease the nonselective binding energy of TALEs. We substituted basic amino acids with alanine in the NTR and identified TALE mutants with increased selectivity. We then analysed conserved, DNA phosphate-binding KQ diresidues in CRD repeats and identified further improved mutants. Combination of mutations in the NTR and CRD was highly synergetic and resulted in TALE scaffolds with up to 4.3-fold increased selectivity in genomic 5mC analysis via affinity enrichment. Moreover, transcriptional activation in HEK293T cells by a TALE-VP64 construct based on this scaffold design exhibited a 3.5-fold increased 5mC selectivity. This provides perspectives for improved 5mC analysis and for the 5mC-conditional control of TALE-based editing constructs in vivo.
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Affiliation(s)
- Preeti Rathi
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Anna Witte
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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41
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Krawczyk K, Demharter S, Knapp B, Deane CM, Minary P. In silico structural modeling of multiple epigenetic marks on DNA. Bioinformatics 2017; 34:41-48. [DOI: 10.1093/bioinformatics/btx516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/22/2017] [Indexed: 12/25/2022] Open
Affiliation(s)
- Konrad Krawczyk
- Department of Computer Science, Oxford University, OX1 3QD Oxford, UK
- Department of Statistics, Oxford University, OX1 3LB Oxford, UK
| | - Samuel Demharter
- Department of Computer Science, Oxford University, OX1 3QD Oxford, UK
| | - Bernhard Knapp
- Department of Statistics, Oxford University, OX1 3LB Oxford, UK
- Faculty of Medicine and Health Sciences, International University of Catalonia, Barcelona, Spain
| | | | - Peter Minary
- Department of Computer Science, Oxford University, OX1 3QD Oxford, UK
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Riml C, Lusser A, Ennifar E, Micura R. Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine. J Org Chem 2017; 82:7939-7945. [PMID: 28707898 DOI: 10.1021/acs.joc.7b01171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
5-Hydroxymethylcytosine (hm5C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm5C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hm5rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hm5rC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hm5rC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hm5rC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hm5rC into the SRL motif resulted in an RNA crystal structure at 0.85 Å resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hm5rC-G pair compared to the unmodified C-G in the native structure was revealed.
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Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria
| | - Eric Ennifar
- Université de Strasbourg, CNRS , Architecture et Réactivité des ARN, UPR 9002, 67000 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
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43
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Demharter S, Knapp B, Deane CM, Minary P. Modeling Functional Motions of Biological Systems by Customized Natural Moves. Biophys J 2017; 111:710-721. [PMID: 27558715 PMCID: PMC5002067 DOI: 10.1016/j.bpj.2016.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 11/30/2022] Open
Abstract
Simulating the functional motions of biomolecular systems requires large computational resources. We introduce a computationally inexpensive protocol for the systematic testing of hypotheses regarding the dynamic behavior of proteins and nucleic acids. The protocol is based on natural move Monte Carlo, a highly efficient conformational sampling method with built-in customization capabilities that allows researchers to design and perform a large number of simulations to investigate functional motions in biological systems. We demonstrate the use of this protocol on both a protein and a DNA case study. Firstly, we investigate the plasticity of a class II major histocompatibility complex in the absence of a bound peptide. Secondly, we study the effects of the epigenetic mark 5-hydroxymethyl on cytosine on the structure of the Dickerson-Drew dodecamer. We show how our customized natural moves protocol can be used to investigate causal relationships of functional motions in biological systems.
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Affiliation(s)
- Samuel Demharter
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Bernhard Knapp
- Department of Statistics, University of Oxford, Oxford, UK
| | | | - Peter Minary
- Department of Computer Science, University of Oxford, Oxford, UK.
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44
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5-Formylcytosine does not change the global structure of DNA. Nat Struct Mol Biol 2017; 24:544-552. [PMID: 28504696 DOI: 10.1038/nsmb.3411] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/13/2017] [Indexed: 01/14/2023]
Abstract
The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognition of clusters of fC. We used NMR and X-ray crystallography to compare several modified DNA duplexes with unmodified analogs and found that in the crystal state the duplexes all belong to the A family, whereas in solution they are all members of the B family. We found that, contrary to previous findings, fC does not significantly affect the structure of DNA, although there are modest local differences at the modification sites. Hence, global conformation changes are unlikely to account for the recognition of this modified base, and our structural data favor a mechanism that operates at base-pair resolution for the recognition of fC by epigenome-modifying enzymes.
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45
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Maurer S, Giess M, Koch O, Summerer D. Interrogating Key Positions of Size-Reduced TALE Repeats Reveals a Programmable Sensor of 5-Carboxylcytosine. ACS Chem Biol 2016; 11:3294-3299. [PMID: 27978710 DOI: 10.1021/acschembio.6b00627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcription-activator-like effector (TALE) proteins consist of concatenated repeats that recognize consecutive canonical nucleobases of DNA via the major groove in a programmable fashion. Since this groove displays unique chemical information for the four human epigenetic cytosine nucleobases, TALE repeats with epigenetic selectivity can be engineered, with potential to establish receptors for the programmable decoding of all human nucleobases. TALE repeats recognize nucleobases via key amino acids in a structurally conserved loop whose backbone is positioned very close to the cytosine 5-carbon. This complicates the engineering of selectivities for large 5-substituents. To interrogate a more promising structural space, we engineered size-reduced repeat loops, performed saturation mutagenesis of key positions, and screened a total of 200 repeat-nucleobase interactions for new selectivities. This provided insight into the structural requirements of TALE repeats for affinity and selectivity, revealed repeats with improved or relaxed selectivity, and resulted in the first selective sensor of 5-carboxylcytosine.
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Affiliation(s)
- Sara Maurer
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227Dortmund, Germany
| | - Mario Giess
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227Dortmund, Germany
| | - Oliver Koch
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227Dortmund, Germany
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46
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47
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Bochtler M, Kolano A, Xu GL. DNA demethylation pathways: Additional players and regulators. Bioessays 2016; 39:1-13. [PMID: 27859411 DOI: 10.1002/bies.201600178] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway. Recent data clarify the roles and the regulation of well-known enzymes in this process. They identify base excision repair (BER) glycosylases that may cooperate with or replace thymine DNA glycosylase (TDG) in the base excision step, and suggest possible involvement of DNA damage repair pathways other than BER in active DNA demethylation. Here, we review these new developments.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kolano
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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48
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Vander Zanden CM, Rowe RK, Broad AJ, Robertson AB, Ho PS. Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Biochemistry 2016; 55:5781-5789. [PMID: 27653243 PMCID: PMC5258817 DOI: 10.1021/acs.biochem.6b00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5-Hydroxymethylcytosine (5hmC) is an epigenetic marker that has recently been shown to promote homologous recombination (HR). In this study, we determine the effects of 5hmC on the structure, thermodynamics, and conformational dynamics of the Holliday junction (the four-stranded DNA intermediate associated with HR) in its native stacked-X form. The hydroxymethyl and the control methyl substituents are placed in the context of an amphimorphic GxCC trinucleotide core sequence (where xC is C, 5hmC, or the methylated 5mC), which is part of a sequence also recognized by endonuclease G to promote HR. The hydroxymethyl group of the 5hmC junction adopts two distinct rotational conformations, with an in-base-plane form being dominant over the competing out-of-plane rotamer that has typically been seen in duplex structures. The in-plane rotamer is seen to be stabilized by a more stable intramolecular hydrogen bond to the junction backbone. Stabilizing hydrogen bonds (H-bonds) formed by the hydroxyl substituent in 5hmC or from a bridging water in the 5mC structure provide approximately 1.5-2 kcal/mol per interaction of stability to the junction, which is mostly offset by entropy compensation, thereby leaving the overall stability of the G5hmCC and G5mCC constructs similar to that of the GCC core. Thus, both methyl and hydroxymethyl modifications are accommodated without disrupting the structure or stability of the Holliday junction. Both 5hmC and 5mC are shown to open the structure to make the junction core more accessible. The overall consequences of incorporating 5hmC into a DNA junction are thus discussed in the context of the specificity in protein recognition of the hydroxymethyl substituent through direct and indirect readout mechanisms.
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Affiliation(s)
- Crystal M. Vander Zanden
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Rhianon K. Rowe
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Amanda J. Broad
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
| | - Adam B. Robertson
- Department of Molecular Microbiology, Sognsvannsveien 20, NO-0027, Oslo University Hospital, Oslo, Norway
| | - P. Shing Ho
- Department of Biochemistry & Molecular Biology, 1870 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1870
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Drohat AC, Coey CT. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA. Chem Rev 2016; 116:12711-12729. [PMID: 27501078 DOI: 10.1021/acs.chemrev.6b00191] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Base excision repair (BER) is one of several DNA repair pathways found in all three domains of life. BER counters the mutagenic and cytotoxic effects of damage that occurs continuously to the nitrogenous bases in DNA, and its critical role in maintaining genomic integrity is well established. However, BER also performs essential functions in processes other than DNA repair, where it acts on naturally modified bases in DNA. A prominent example is the central role of BER in mediating active DNA demethylation, a multistep process that erases the epigenetic mark 5-methylcytosine (5mC), and derivatives thereof, converting them back to cytosine. Herein, we review recent advances in the understanding of how BER mediates this critical component of epigenetic regulation in plants and animals.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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50
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Rathi P, Maurer S, Kubik G, Summerer D. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity. J Am Chem Soc 2016; 138:9910-8. [PMID: 27429302 DOI: 10.1021/jacs.6b04807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases.
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Affiliation(s)
- Preeti Rathi
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Sara Maurer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Grzegorz Kubik
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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