Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping

Nucleic Acids Research, vol. 50, pp. e92

Abstract

DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500-1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.

Authors 13

1. Tslil Gabrieli

   Tel Aviv University

   Affiliation as printed

   School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel

2. Yael Michaeli

   Tel Aviv University

   Affiliation as printed

   School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel

3. Sigal Avraham

   Tel Aviv University

   Affiliation as printed

   School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel

4. Dmitry Torchinsky

   Tel Aviv University

   Affiliation as printed

   School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel

5. Sapir Margalit

   Tel Aviv University

   Affiliation as printed

   School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel

6. Leonie Schütz Aachen Institute of Organic Chemistry

   RWTH Aachen University

   Affiliation as printed

   Institute of Organic Chemistry, RWTH Aachen University , D-52056 Aachen , Germany

7. Matyas Juhasz Aachen Institute of Organic Chemistry

   RWTH Aachen University

   Affiliation as printed

   Institute of Organic Chemistry, RWTH Aachen University , D-52056 Aachen , Germany

8. Ceyda Çoruh

   Salk Institute for Biological Studies

   Affiliation as printed

   Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies , La Jolla , CA , USA

9. Nissim Arbib

   Tel Aviv University · Meir Medical Center

   Affiliation as printed

   Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel

10. Zhaohui Sunny Zhou

    Northeastern University

    Affiliation as printed

    Department of Chemistry and Chemical Biology, and Barnett Institute of Chemical and Biological Analysis, Northeastern University , Boston , Massachusetts 02115 , USA

11. Julie A. Law

    Salk Institute for Biological Studies

    Affiliation as printed

    Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies , La Jolla , CA , USA

12. Elmar G. Weinhold corresponding Aachen Institute of Organic Chemistry

    RWTH Aachen University

    Affiliation as printed

    Institute of Organic Chemistry, RWTH Aachen University , D-52056 Aachen , Germany

13. Yuval Ebenstein corresponding

    Tel Aviv University

    Affiliation as printed

    School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv , Israel