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Sharim H, Grunwald A, Gabrieli T, Michaeli Y, Margalit S, Torchinsky D, Arielly R, Nifker G, Juhasz M, Gularek F, Almalvez M, Dufault B, Chandra SS, Liu A, Bhattacharya S, Chen YW, Vilain E, Wagner KR, Pevsner J, Reifenberger J, Lam ET, Hastie AR, Cao H, Barseghyan H, Weinhold E, Ebenstein Y. Long-read single-molecule maps of the functional methylome. Genome Res 2019; 29:646-656. [PMID: 30846530 PMCID: PMC6442387 DOI: 10.1101/gr.240739.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 02/25/2019] [Indexed: 01/23/2023]
Abstract
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs. The method provides kilobase pair–scale genomic methylation patterns comparable to whole-genome bisulfite sequencing (WGBS) along genes and regulatory elements. These long single-molecule reads allow for methylation variation calling and analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell second-generation sequencing. The method is applied here to study facioscapulohumeral muscular dystrophy (FSHD), simultaneously recording the haplotype, copy number, and methylation status of the disease-associated, highly repetitive locus on Chromosome 4q.
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Affiliation(s)
- Hila Sharim
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Assaf Grunwald
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Sapir Margalit
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Rani Arielly
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Gil Nifker
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Matyas Juhasz
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Miguel Almalvez
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Brandon Dufault
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Sreetama Sen Chandra
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Alexander Liu
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Kathryn R Wagner
- Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Ernest T Lam
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Alex R Hastie
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Han Cao
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
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