100 cells were enough to analyze the epigenome
100 cells were enough to analyze the epigenome
Scientists from several US institutes have created a microfluidic device that allows chromatin analysis from a record small number of cells. For example, the new method may allow epigenetic (i.e. related to protein modifications of DNA) studies of embryonic stem cells at an early stage of development. The work is published in Nature Methods (A microfluidic device for epigenomic profiling using 100 cells).
The new technology included several main stages. Initially, the authors placed colloidal particles with grafted antibodies specific to the analyzed chromatin proteins into the microchannel. Next, a solution of fragmented DNA cross-linked with chromatin proteins was injected into the channel, which were adsorbed on microparticles due to interaction with antibodies.
In order to wash the DNA-protein-microparticle complex from "excess" material, the entire device was shaken, while pumping a clean buffer solution through the channel. After washing, microparticles with adsorbed proteins and DNA fragments were collected, protein and nucleic acid complexes were "stitched" and DNA sequenced.
The authors tested the new technology by analyzing hemocytoblasts from the liver of a mouse embryo. These cells are the early precursors of blood cells. At an early stage of fetal development, they are very difficult to obtain in large quantities, which makes it difficult to analyze them. Using the new technology, it was possible to isolate the necessary DNA fragments from a sample that included only 100 cells.
Schematic diagram of chromatin isolation due to interaction with antibodies grafted to microparticles.
Image: Zhenning Cao et al./ Nature Methods
The experiment described in this paper is a modification of chromatin immunoprecipitation. This method is used to analyze specific interactions of DNA with proteins, for example, histones. The method is based on the chemical "crosslinking" of proteins with DNA, the destruction of nucleic acid by ultrasound and the subsequent isolation of DNA fragments due to specific antibodies.
Similar methods are used both in basic research and in medical diagnostics. Their wide distribution is difficult, since traditional methods require a very large number of cells, about 10 7. The new technology can significantly reduce this number and make epigenetic research more accessible.
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29.07.2015