Detecting Epigenetic Marks on Opposing DNA Strands

Tech ID: 32467 / UC Case 2021-971-0


Direct modifications to DNA (ex. 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, 5-carboxylcytosine, N6-methyladenine)  play a vital role during human development and in disease progression, including cancers. These epigenetic marks do not always exist in a complementary manner on opposing strands of the same double-stranded DNA. However, the presence or absence of complementary modifications provides novel biological insights into the epigenetic state of a system. For even the most well-studied DNA modification, 5-methylcytosine, current technologies that render such measurements are inefficient, requiring high input DNA, thereby limiting their applications. Additionally, existing technologies are limited in which DNA modifications can be profiled on opposing DNA strands. 


Researchers at the University of California, Santa Barbara, have developed a highly sensitive, genome-wide methodology for analyzing modifications to DNA on opposing strands that works with very low input; even single-cell samples. This technology enables simultaneous detection of DNA modifications on both strands at a single nucleotide resolution, utilizing next-generation DNA sequencing as its readout. The invention can detect the absence or presence of 5-methylcytosine on both DNA strands, down to the resolution of individual cells. Additional experiments demonstrate the detection of 5-hydroxymethylcytosine on one DNA strand and 5-methylcytosine on the opposing strand. This technology is modular and can work with any modification-dependent endonuclease. It can also work with any approach that introduces a point mutation in the DNA sequence to read out the absence or presence of a direct modification to DNA through sequencing. This technology can be applied to fundamental and clinical research of novel disease biomarkers from patient-derived samples where the material is limited. Additionally, this invention allows for high-throughput multiplexing of samples (or single cells), simplifying library construction and lowering costs.


  • Low starting input DNA 
  • Provides information on DNA modifications on opposing strands in addition to traditional bisulfite sequencing data
  • Uses commercially available materials and reagents
  • Broad R&D applications
  • Lower costs


  • Kits for fundamental research in industry and academia 
  • Molecular diagnostics (oncology, for example)
  • Epigenomic editing validation

Patent Status

Patent Pending


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  • Chialastri, Alex
  • Dey, Siddharth

Other Information


DNA, DNA modification, DNA sequencing, detection, biomarkers, Molecular diagnostic, Epigenetic mark, Epigenetic

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