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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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Singh H, Das CK, Buchmuller BC, Schäfer LV, Summerer D, Linser R. Epigenetic CpG duplex marks probed by an evolved DNA reader via a well-tempered conformational plasticity. Nucleic Acids Res 2023; 51:6495-6506. [PMID: 36919612 PMCID: PMC10325892 DOI: 10.1093/nar/gkad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/14/2023] [Accepted: 02/15/2023] [Indexed: 03/16/2023] Open
Abstract
5-methylcytosine (mC) and its TET-oxidized derivatives exist in CpG dyads of mammalian DNA and regulate cell fate, but how their individual combinations in the two strands of a CpG act as distinct regulatory signals is poorly understood. Readers that selectively recognize such novel 'CpG duplex marks' could be versatile tools for studying their biological functions, but their design represents an unprecedented selectivity challenge. By mutational studies, NMR relaxation, and MD simulations, we here show that the selectivity of the first designer reader for an oxidized CpG duplex mark hinges on precisely tempered conformational plasticity of the scaffold adopted during directed evolution. Our observations reveal the critical aspect of defined motional features in this novel reader for affinity and specificity in the DNA/protein interaction, providing unexpected prospects for further design progress in this novel area of DNA recognition.
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Affiliation(s)
- Himanshu Singh
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Benjamin C Buchmuller
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
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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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4
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Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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5
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Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M. Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. Nucleic Acids Res 2021; 49:1708-1723. [PMID: 33450012 PMCID: PMC7897488 DOI: 10.1093/nar/gkaa1218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/28/2022] Open
Abstract
Many modification-dependent restriction endonucleases (MDREs) are fusions of a PUA superfamily modification sensor domain and a nuclease catalytic domain. EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA. The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. It flips the modified nucleotide, to accommodate it in a hydrophobic pocket of the enzyme, primarily formed by P24, W82 and Y130 residues. In the crystallized conformation, the EVE domain and linker helix between the two domains block DNA binding to the catalytic domain. Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues.
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Affiliation(s)
- Michal Pastor
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Igor Helbrecht
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Krakowska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Thomas Lutz
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Tam BE, Hao Y, Sikes HD. An examination of critical parameters in hybridization-based epigenotyping using magnetic microparticles. Biotechnol Prog 2018; 34:1589-1595. [PMID: 29693329 DOI: 10.1002/btpr.2644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/14/2018] [Indexed: 12/24/2022]
Abstract
Gene-specific promoter methylation is involved in gene silencing and is an important cancer biomarker. Cancer-specific methylation patterns have been observed and clinically validated for numerous gene promoters, but the knowledge gleaned from this large body of work is currently under-utilized in the clinic. Methylation-specific PCR is currently the gold standard method for clinical methylation assessment, but several research groups have proposed hybridization-based techniques which could be simpler to implement and provide more accurate results. However, the sensitivity of this easier alternative must be improved dramatically in order to compete with methylation-specific PCR. Efficient sample capture is a key step in maximizing sensitivity, so here we investigate the key parameters involved in (i) maximizing the capture of gene-specific target DNA molecules at the surfaces of functionalized, magnetic microparticles and (ii) recognizing DNA methylation using an engineered methyl-CpG-binding domain (MBD) protein. The magnetic bead density, the probe concentration, and the MBD concentration were very important for maximizing detection, and other variables such as the hybridization time also impacted the target capture efficiency but had a smaller effect on the overall methylation assay. The effect of genomic DNA on the capture of the target sequence was also investigated, and model methylated vs. unmethylated target sequences could be distinguished in the presence of 1 ng/μL genomic DNA. The findings we report related to the underlying binding events involved in hybridization-based epigenotyping can be leveraged in combination with the many signal amplification and detection approaches that are currently being developed. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1589-1595, 2018.
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Affiliation(s)
- Brooke E Tam
- Dept. of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
| | - Yining Hao
- Dept. of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
| | - Hadley D Sikes
- Dept. of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139
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