Toward single-cell epigenome analysis: A microfluidic device for isolating, stretching, and imaging individual chromosomes

Abstract

We developed a microfluidic device with microstructures that can moor the ends of chromatin fibers obtained by unfolding single intact chromosomes. This mooring involves trapping both ends of the chromosome with antibody-conjugated microspheres and placing each microsphere on the microstructure. In principle, the device is structured in such a way that mooring of chromatin fibers, i.e., partially unfolded chromosomes, is achieved under uniform tension, which is necessary to obtain an accurate distribution of folded/unfolded regions and fluorescence probes on the chromatin fibers. In addition, changes in the distribution of chromatin folding structures were observed by controlling the solution conditions, and specific histone chemical modification regions were visualized by immunofluorescence staining of chromatin fibers in the elongated form with uniform tension. This method is advantageous for the epigenetic analysis of non-fragmented natural chromatin fibers.