A team of researchers, led by Professors Yanyi Huang and Fuchou Tang of Biodynamic Optical Imaging Center at Peking University developed a new microfluidic-based method for DNA capture from minute number of cells. They implemented a microfluidic device to facilitate the Chromatin Immunoprecipitation (ChIP) process, providing a technology to obtain the high-quality ChIP-Seq data from merely 1,000 mammalian cells, with no need of pre-amplification. They have accomplished, for the first time, a rapid, semi-automated, and highly sensitive ChIP assay to investigate the genome-wide landscape of histone modification H3K4me3 using 1 000 mouse epiblast cells at E6.5, and found that the H3K4me3 landscape of post-implantation epiblast is more similar to that of the mEpiSCs than that of mESCs. The research is published on Cell Research on Sep. 2nd, 2014.

ChIP-Seq is one of the most widely used approaches in investigating transcription regulation and demonstrating epigenetic mechanism. DNA binding to certain proteins would be captured and enriched by targeting the specific proteins. The DNA obtained can subsequently be applied to high-throughput sequence, in order to investigate the interaction and binding sites between DNA and protein.

With specifically designed microfluidic device, the key steps in ChIP, covalent linkage of chromatin with antibody-bead complex and washing of non-covalent binding, were integrated onto a single micro-device, enabling multi-sample assays at the same time. This technology considerably decreases the sample amount requirement to 1,000 cells, while 10^6 cells are needed in conventional protocols. This not only benefits the efficiency and time saving of the assay, but also reduces sample loss and error during operation, which reassures higher reliability and better reproducibility.

The group investigated H3K4me3 modification in mouse embryo stem cell, mEpiSCs and mouse epiblast cells at E6.5. ChIP-Seq of 1,000 cells enriches 12,000 to 20,000 transcriptional start sites (TSS), more than 96% of which could overlap with bulk cell results, indicating that the method is more sensitive and has less false positive results. The mean correlation coefficient is 0.94 when comparing the H3K4me3 profile of various samples. Compared with mESCs, both epiblast cells of E6.5 mouse embryos and mEpiSCs enriched for the ectodermal differentiation-related characteristics such as neural tube development and neuronal differentiation. This work exhibited ChIP-Seq results of minute amount of cells, which requires least cell number compared to previous approaches, without pre-amplification before library.

This breakthrough in technology would considerably facilitate our understanding of unrevealed issues in developmental biology. Moreover, the method could be applied to various areas such as cancer, immunology and neuroscience, realizing subtle observation and analysis of epigenetic characteristic.

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Original Paper

J. Shen, D. Jiang, Y. Fu, X. Wu, H. Guo, B. Feng, Y. Pang, A. M. Streets, F. Tang, and Y. Huang, “H3K4me3 epigenomic landscape derived from ChIP-Seq of 1 000 mouse early embryonic cells.,” Cell Res., pp. 1–5, Sep. 2014.