Beyond the Sequence – Single-Molecule Epigenomics

Yuval Ebenstein, School of Chemistry, Tel Aviv University, Tel Aviv, Israel

Next generation sequencing (NGS) is revolutionizing all fields of biological research but it fails to extract the full range of information associated with genetic material and is lacking in its ability to resolve variations between genomes. Chromosomes contain a plethora of variable regions that include single point mutations (SNP), structural variations (SV), copy number variations (CNV) and DNA repeats. In addition, the information content of the genome extends beyond the base sequence in the form of chemical modifications such as DNA methylation or DNA damage lesions. By regarding chromosomes as single molecules and applying experimental principles of single molecule detection we gain access to the structural variation and long range patterns of genetic and epigenetic information. We show how physical extension of long DNA molecules on surfaces and in nanofluidic channels reveals such information in the form of a linear, optical “barcode”, like beads threaded on a string, where each bead represents a distinct type of observable. Recent results from our lab demonstrate our ability to detect the epigenetic mark 5-hydroxymethylcytosine and various forms of DNA damage on individual genomic DNA molecules. As well as detecting and quantifying DNA damage on the single molecule level