When less is more: A promising approach for low-cell-number epigenomic profiling


Credit: Yuko Sato (Tokyo Institute of Technology)

Scientists at Kyushu University and Tokyo Institute of Technology in Japan have developed a technique that enables analysis of DNA-protein interactions using very small numbers of cells, ranging from 100 to 1,000. Their method could capture previously unexamined epigenomic information, facilitate biomarker discovery and open new avenues for precision medicine.

A collaborative study by researchers at Kyushu University, Tokyo Institute of Technology, Waseda University, the University of Tokyo and Osaka University has led to the development of a unique approach to epigenomic profiling[1] that involves working with much fewer cells than in existing methods.

The technique, called Chromatin Integration Labeling sequencing (ChIL-seq), could open up new opportunities for scientists to study rare cell types and other cell samples in short supply. ChIL-seq requires only a fraction of starting cellular material. In a series of experiments to evaluate ChIL-seq performance, the researchers success-fully demonstrated detection of histone modifications[2] and DNA-binding factors using just 100 to 1,000 cells.

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, one limitation has been that ChIP-seq requires at least 10,000 or typically millions of cells to start off with, mainly due to the fact that samples tend to be lost during two key steps: chromatin preparation[3] and immunoprecipitation[4].

The research team, co-led by Hiroshi Kimura of the Institute of Innovative Research, Tokyo Institute of Technology, and Yasuyuki Ohkawa of Medical Institute of Bioregulation, Kyushu University, overcame the problem of sample loss by replacing the two steps mentioned above with immunostaining, a non-destructive method suitable for analyzing tissue specimens.

Using ChIL-seq, the team also detected genomic regions associated with histone marks at the single-cell level — an achievement that brings biologists closer to the long-held goal of establishing single-cell profiling.

ChIL-seq can “zoom in” on genomic sequences near target molecules before cellular breakdown, and this is particularly useful for studying adherent cells, i.e., whole cells that remain attached to culture plates and after immunofluorescence.

Many different types of epigenome profiling methods are now being developed around the world. Each has its advantages and limitations. The researchers point out that ChIL-seq, too, still needs refining. In its current form, for example, it has low sensitivity to heterochromatin regions, and it can take 3-4 days to complete the procedure.

Overall, they are 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.


Technical terms

[1] Epigenomic profiling: Analysis of DNA-protein interactions that can provide in-sights into disease states and therapeutic targets.

[2] Histone modifications: Post-translational modifications that regulate gene expression.

[3] Chromatin preparation: A process involving the extraction of information-rich chromatin (a complex of DNA and proteins) through the breakdown of cells.

[4] Immunoprecipitation: Purification of target proteins based on the antigen-antibody interaction.

Related links



Catching histones by the tail: a new probe to track histone modifications in living cells



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Kyushu University

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Emiko Kawaguchi

Public Relations Section,

Tokyo Institute of Technology

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General Affairs Team

Institute for Quantitative Biosciences

The University of Tokyo

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Tetsu Kawaguchi

Life Innovation Group, Department of Innovation Research

Japan Science and Technology Agency (JST)

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About Kyushu University

Kyushu University is a comprehensive and one of the top research universities in Japan. The university is located in Fukuoka, which is historically renowned as Japan’s gateway to Asia for profound cultural and economic interactions due to its geographical proximity to continental Asia.

Kyushu University is comprised of 12 undergraduate schools, 18 graduate schools, 17 faculties, 5 research institutes, University hospital and library, as well as over 50 affiliated research centers. It is recognized as an international university, it has an enrollment of about 20,000 students including more than 2,000 international students from over 100 countries. For more information, please visit its website http://www.kyushu-u.ac.jp/en/

About Tokyo Institute of Technology

Tokyo Institute of Technology stands at the forefront of research and higher education as the leading university for science and technology in Japan. Tokyo Tech re-searchers excel in a variety of fields, such as material science, biology, computer science and physics. Founded in 1881, Tokyo Tech has grown to host 10,000 under-graduate and graduate students who become principled leaders of their fields and some of the most sought-after scientists and engineers at top companies. Embodying the Japanese philosophy of “monotsukuri,” meaning technical ingenuity and innovation, the Tokyo Tech community strives to make significant contributions to society through high-impact research. http://www.titech.ac.jp/english/

About the University of Tokyo

The University of Tokyo is Japan’s leading university and one of the world’s top re-search universities. The vast research output of some 6,000 researchers is published in the world’s top journals across the arts and sciences. Our vibrant student body of around 15,000 undergraduate and 15,000 graduate students includes over 2,000 international students.

Find out more at http://www.u-tokyo.ac.jp/en/ or follow us on Twitter at @UTokyo_News_en.

About Japan Science and Technology Agency (JST)

JST is an organization that leads Japan’s science and technology (S&T) development as an innovation navigator. We aim to contribute to the lives of people and the achievement of a sustainable society by promoting S&T for the purpose of opening up opportunities in innovation. Since its foundation, JST’s many outstanding achievements accomplished in collaboration with the government, universities, the industrial sector and public have been earned global recognition.


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