Single molecule epigenetic analysis in a nanofluidic channel

Benjamin R. Cipriany, Ruqian Zhao, Patrick J. Murphy, Stephen L. Levy, Christine P. Tan, Harold G. Craighead, Paul D. Soloway

    Research output: Contribution to journalArticlepeer-review

    100 Scopus citations

    Abstract

    Epigenetic states are governed by DNA methylation and a host of modifications to histones bound with DNA. These states are essential for proper developmentally regulated gene expression and are perturbed in many diseases. There is great interest in identifying epigenetic mark placement genome wide and understanding how these marks vary among cell types, with changes in environment or according to health and disease status. Current epigenomic analyses employ bisulfite sequencing and chromatin immunoprecipitation, but query only one type of epigenetic mark at a time, DNA methylation, or histone modifications and often require substantial input material. To overcome these limitations, we established a method using nanofluidics and multicolor fluorescence microscopy to detect DNA and histones in individual chromatin fragments at about 10 Mbp/min. We demonstrated its utility for epigenetic analysis by identifying DNA methylation on individual molecules. This technique will provide the unprecedented opportunity for genome wide, simultaneous analysis of multiple epigenetic states on single molecules.

    Original languageEnglish (US)
    Pages (from-to)2480-2487
    Number of pages8
    JournalAnalytical Chemistry
    Volume82
    Issue number6
    DOIs
    StatePublished - Mar 15 2010

    ASJC Scopus subject areas

    • Analytical Chemistry

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