Whole-Genome Profiling of CpG Methylation in Arabidopsis thaliana By Single-Molecule Genome Mapping in Nanochannels Arrays

Single-molecule Genome mapping is based on stretching genomic DNA molecules by squeezing them into an array of silicon nanochannels. When the DNA is fluorescently labeled at specific sequence motifs, long (50-1000Kbp) individual DNA molecules are imaged by a fluorescence microscope as linear fluorescent barcodes that report on the genomic locus of the molecules and on any structural variation from the genome reference. Here, we add epigenetic information to this genetic analysis method by highlighting DNA methylation patterns along the molecules

Due to the dynamic nature of the methylation process, DNA methylation patterns exhibit a large degree of inter-individual variance. This heterogeneity in the methylation state across individual cells (even in the same tissue) makes epigenetic analysis on the single cell and single genome level a necessity. Such analysis is hindered by the limitations of existing DNA array and sequencing based technologies that provide population averaged profiles of DNA methylation. Despite recent advances in single-cell sequencing, these technologies are inherently problematic in combining methylation patterns with structural variation or repetitive elements which compose large fractions of mammal and plant genomes.

We establish a new enzymatic labeling method that differentiates between methylated and unmethylated cytosines in CpG dinucleotides. Unmethylated cytosines are fluorescently tagged for whole genome methylation mapping of individual genomic fragments.

By combining our methylation profiling method with site specific genetic labeling we were able to map the genome-wide methylation profile of Arabidopsis Thaliana and simultaneously capture large scale genetic variations such as tandem repeats.