Long-read single-molecule maps of the functional methylome
- Hila Sharim1,6,
- Assaf Grunwald1,6,
- Tslil Gabrieli1,
- Yael Michaeli1,
- Sapir Margalit1,
- Dmitry Torchinsky1,
- Rani Arielly1,
- Gil Nifker1,
- Matyas Juhasz2,
- Felix Gularek2,
- Miguel Almalvez3,
- Brandon Dufault3,
- Sreetama Sen Chandra3,
- Alexander Liu3,
- Surajit Bhattacharya3,
- Yi-Wen Chen3,
- Eric Vilain3,
- Kathryn R. Wagner4,
- Jonathan Pevsner4,
- Jeff Reifenberger5,
- Ernest T. Lam5,
- Alex R. Hastie5,
- Han Cao5,
- Hayk Barseghyan3,
- Elmar Weinhold2 and
- Yuval Ebenstein1
- 1School 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;
- 2Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany;
- 3Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA;
- 4Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
- 5Bionano Genomics, Inc., San Diego, California 92121, USA
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↵6 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.240739.118.
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Freely available online through the Genome Research Open Access option.
- Received June 14, 2018.
- Accepted February 25, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
