Editors' ChoiceStem Cells

Singled out: Exploring epigenetics

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Science Translational Medicine  11 Nov 2015:
Vol. 7, Issue 313, pp. 313ec195
DOI: 10.1126/scitranslmed.aad5512

How do genetically identical cells develop and maintain their distinct phenotypes? Conrad Waddington originally envisioned undifferentiated cells as marbles rolling down a rugged epigenetic landscape. Marbles start at the same location but travel different trajectories to various nooks and crannies associated with particular cell fates. Molecularly, these epigenetic explorations occur through chemical modifications of chromatin structure, encoding the memory and transmission of phenotypic traits without altering DNA sequence. The heterogeneity and stability of these chromatin states can vary considerably, making them challenging to measure with conventional bulk assays such as CHiP-seq. By measuring the average signal of a large population, these assays reveal a flat featureless plateau rather than the subtle details of the landscape.

Rotem et al. used droplet-based microfluidics and DNA barcoding to measure the chromatin state of thousands of individual cells. First, cells from a mixed population of mouse embryonic stem cells, fibroblasts, and hematopoetic progenitors were individually encapsulated within an aqueous droplet, lysed, and their chromosomes enzymatically digested into chromatin fragments. Next, the authors labeled the chromatin fragments from each drop with a barcode adaptor that specified the cell of origin and provided a handle for PCR amplification. Sequencing of the fragments from single cells allowed the authors to define the distinct epigenetic profiles of the cells within the mixed population, which aligned with bulk ChiP-seq data from isolated subpopulations. Moreover, the enhanced resolution of this approach revealed three previously unidentified subpopulations of embryonic stem cells that varied by pluripotent potential.

This use of microfluidic droplets to compartmentalize single cells enables ChiP-seq measurements at high throughput with greatly reduced reagent consumption and cost. Overall, this new approach illuminates the detailed landscape of epigenetic transitions in development and disease. When combined with targeted epigenetic inhibitors, these measurements could improve the reprogramming of induced pluripotent stem cells, as well as identify new biomarkers for the diagnosis, prognosis, and therapeutic monitoring of cancer.

A. Rotem et al., Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165–1172 (2015). [Abstract]

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