Long-read single-molecule maps of the functional methylome
- Hila Sharim1,
- Assaf Grunwald1,
- 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 Ebenstein1,6
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 (kbp). The method provides kbp-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.
- Received June 14, 2018.
- Accepted February 25, 2019.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
