Fewer Cells But Greater Precision

A research group in Japan has developed a technique to perform epigenomic profiling with much fewer cells than existing methods.

AsianScientist (Dec. 24, 2018) – Scientists in Japan have developed a technique that enables analysis of DNA-protein interactions using very small numbers of cells. They published their method in the journal Nature Cell Biology.

For the past decade, chromatin immunoprecipitation sequencing (ChIP-seq) has been the dominant technique for analyzing epigenomic data and identifying important binding sites of DNA-associated proteins. However, a key limitation of ChIP-seq is that the method typically requires at least 10,000 or millions of cells for accurate analysis. This is because samples tend to be lost during two key steps: chromatin preparation and immunoprecipitation.

In the present study, a team of scientists led by Professor Hiroshi Kimura of the Tokyo Institute of Technology, Japan, and Professor Yasuyuki Ohkawa of Kyushu University, Japan, overcame the problem of sample loss by replacing chromatin preparation and immunoprecipitation with immunostaining, a non-destructive method suitable for analyzing tissue specimens. They called their technique chromatin integration labeling sequencing (ChIL-seq).

ChIL-seq requires only a fraction of starting cellular material. In a series of experiments to evaluate ChIL-seq performance, the researchers successfully demonstrated detection of histone modifications and DNA-binding factors using just 100 to 1,000 cells. With this technique, the researchers were able to detect genomic regions associated with histone marks at the single-cell level, bringing biologists closer to the ideal of carrying out single-cell profiling.

Importantly, ChIL-seq can ‘zoom in’ on genomic sequences near target molecules before cellular breakdown, a characteristic that is particularly useful for studying cells that remain attached to culture plates.

Nonetheless, the researchers note that ChIL-seq still needs to be refined. In its current form, for example, ChIL-seq has low sensitivity to heterochromatin regions and it can take three to four days to complete the procedure.

The team remains confident that ChIL-seq holds promise due to its precision, which makes it suitable for single-cell applications, and its flexibility, meaning that in future, it could be combined with other powerful sequencing techniques.

The article can be found at: Harada et al. (2018) A Chromatin Integration Labelling Method Enables Epigenomic Profiling with Lower Input.


Source: Tokyo Institute of Technology; Photo: Yuko Sato.
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