A*STAR's Genome Institute of Singapore Develops Advanced Method to Study Epigenome of Cells Essential for Normal Growth and Development

Published: Feb 11, 2013

February 11, 2013 -- Scientists at A*STAR’s Genome Institute of Singapore (GIS) have successfully developed a method to map the epigenome using 100 times fewer cells than was previously possible. The discovery, published in the journal Developmental Cell, means that it is now possible to study the epigenome of parts of the body with rare cell populations such as germ cells (which differentiate into the egg or sperm), and clinical biopsy samples (to advance the study, diagnosis and prevention of cancer).

This is an extremely important advancement since the proper regulation of the epigenome is essential for normal growth and health, while any abnormality in the regulation could be the cause of diseases such as cancers.

The genome, which refers to the complete set of DNA (deoxyribonucleic acid) in a cell, is identical in every cell of an individual’s body. Chemical markers (also known as epigenetic markers) target the genome and influence which genes get turned on or off. It is the turning on or off of the genes that gives rise to the existence of different cells in the body, even though the genomes are identical. The epigenome refers to the record of these chemical changes that occur to the DNA. Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) is a commonly used method to study the epigenome of cells. In ChIP-Seq, DNA fragments that are associated with specific epigenetic marks are baited out, sequenced and mapped to a reference genome. However, the conventional method typically requires large quantities of cells, which makes it difficult to study rare cell populations of the body or in precious clinical biopsy samples.

This limitation prompted the GIS scientists to miniaturize the ChIP method such that it is now possible to map the epigenome using much fewer cells (1,000 to 100,000 cells). The conventional method required one million to 10 million cells.

The scientists further applied this technology on a small number of mouse germ cells, which are the embryonic precursors of the sperm and egg, and uncovered many interesting epigenomic features that provide insight into the biology of the germ cells.

GIS Executive Director Prof Ng Huck Hui said, “Epigenomics is an exciting frontier for human biology research. While the sequence of human genome tells us the code for life, it doesn’t tell us how this code is utilized. The mystique of the epigenome lies in the multiple forms it takes and the remarkable information that it harbours. At the Genome Institute of Singapore, we are investing efforts to develop new microscale technologies to analyse the epigenomes of human cells and tissues.”

"The new ChIP-seq protocol allows us to map the epigenomes of very small populations of cells that are not accessible by conventional methods,” said GIS Principal Investigator Dr Shyam Prabhakar. “It's akin to having a more powerful microscope that provides a more fine-grained view of critical biological processes. We are very excited about using this new technique to peer into the inner workings of tiny groups of cells that have a massive impact on human health. For example, tumours in cancer patients are known to be heterogeneous at the fine scale - some sub-regions are relatively benign, while others are lethal. The new protocol will help us characterize this fine-scale variation, and hopefully lead to more precise treatments for cancer and a host of other diseases."

Commercial development of the Microscale Epigenomics Technology project was funded by A*STAR’s technology transfer arm, ETPL (Exploit Technologies Pte Ltd), for comparison and validation studies prior to licensing the technology to a local biotechnology company, SG Microlab Devices for the academic research market.

Research publication:

The research findings described in the press release was published online in January 2013, and can be found in the 11th February 2013 print issue of Developmental Cell under the title “In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures”.


Jia-Hui Ng1,2,* Vibhor Kumar3,* Masafumi Muratani1,* Petra Kraus4, Jia-Chi Yeo1,7 Lai-Ping Yaw1, Kun Xue1, Thomas Lufkin4, Shyam Prabhakar3,#, and Huck-Hui Ng1,5,6,7,#

1. Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672

2. NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456

3. Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672

4. Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672

5. Dept of Biochemistry, National University of Singapore, Singapore 117597

6. Dept of Biological Sciences, National University of Singapore, Singapore 117543

7. School of Biological Sciences, Nanyang Technological University, Singapore 637551

* These authors contributed equally to this work.

Corresponding Authors:

Huck-Hui Ng nghh@gis.a-star.edu.sg;

Shyam Prabhakar prabhakars@gis.a-star.edu.sg.


Winnie Lim

Genome Institute of Singapore

Office of Corporate Communications

Tel: (65) 6808 8013

Email: limcp2@gis.a-star.edu.sg

About the Genome Institute of Singapore (GIS)

The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to improve public health and public prosperity. Established in 2001 as a centre for genomic discovery, the GIS will pursue the integration of technology, genetics and biology towards the goal of individualized medicine.

The key research areas at the GIS include Systems Biology, Stem Cell & Developmental Biology, Cancer Biology & Pharmacology, Human Genetics, Infectious Diseases, Genomic Technologies, and Computational & Mathematical Biology. The genomics infrastructure at the GIS is utilized to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact. www.gis.a-star.edu.sg

About the Agency for Science, Technology and Research (A*STAR)

The Agency for Science, Technology and Research (A*STAR) is Singapore's lead public sector agency that fosters world-class scientific research and talent to drive economic growth and transform Singapore into a vibrant knowledge-based and innovation driven economy.

In line with its mission-oriented mandate, A*STAR spearheads research and development in fields that are essential to growing Singapore’s manufacturing sector and catalysing new growth industries. A*STAR supports these economic clusters by providing intellectual, human and industrial capital to its partners in industry.

A*STAR oversees 20 biomedical sciences and physical sciences and engineering research entities, located in Biopolis and Fusionopolis as well as their vicinity. These two R&D hubs house a bustling and diverse community of local and international research scientists and engineers from A*STAR’s research entities as well as a growing number of corporate laboratories.


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