New technique allows biologists to profile patterns of gene regulation in rare cell populations

May 22, 2013
Genomics: A rare view of gene regulation
Epigenetic changes to chromosome structure influence whether or not certain genes are active. Credit: Dorling Kindersley RF/Thinkstock

Mapping all of the chemical, or epigenetic, changes to chromosomes that affect which genes are turned on or off—and thus determine the fate of genomically identical cells in the body—usually requires a large amount of starting cellular material. This technical limitation has impeded the analysis of gene regulation in many rare cell types and in small clinical biopsy samples. Now, a team of biologists led by A*STAR scientists has developed a protocol for characterizing these changes that requires up to 100 times fewer cells than previously needed. As a proof of principle, the researchers used the approach to chart which genes are activated or repressed in mouse reproductive cells that eventually give rise to eggs or sperm.

"We developed a technique for epigenetic analysis of very small numbers of cells, and used it to identify gene in the genome of in the ," says one of the team leaders, Shyam Prabhakar from A*STAR's Genome Institute of Singapore.

The team, which is co-led by the Genome Institute of Singapore's Huck Hui Ng, started with a standard technique for epigenetic analysis known as ChIP-seq. This method combines a way of investigating the interactions between proteins and DNA called 'chromatin immunoprecipitation', or ChIP, with high-throughput DNA sequencing. ChIP-seq can reveal modifications to chromosome structures that affect (see image). Typically, ChIP-seq requires millions of cells to work properly. Prabhakar and Ng's team, however, adapted the technique so that it could work with just 10,000 cells. This involved miniaturizing various aspects of the protocol so that it worked reliably with smaller volumes.

Using the small-scale ChIP-seq method on germ cells taken from embryonic mice, the researchers revealed many previously unknown epigenetic features needed for proper maintenance and development of these early precursors of eggs and sperm. They include changes to promoters and enhancer elements that control how germ-cell specific genes are activated, as well as repressive marks on some genes that are needed only later in development. Interestingly, the analysis also showed that genetic elements called retrotransposons and genes involved in activating immune responses are both silenced, preserving genomic integrity and preventing cell death in these important .

Next, Prabhakar, Ng and co-workers plan to apply the method to study rare cell populations in humans, including biopsies taken from cancer patients. "This technology now enables us to study other cell types of limited quantity," Ng says.

Explore further: Two-armed control of ATR, a master regulator of the DNA damage checkpoint

More information: Ng, J.-H., Kumar, V., Muratani, M., Kraus, P., Yeo, J.-C. et al. In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Developmental Cell 24, 324–333 (2013). www.cell.com/developmental-cel… ii/S1534580712005850

add to favorites email to friend print save as pdf

Related Stories

Mapping the embryonic epigenome

May 09, 2013

A large, multi-institutional research team involved in the NIH Epigenome Roadmap Project has published a sweeping analysis in the current issue of the journal Cell of how genes are turned on and off to direct early human ...

Scientists shed light on the 'dark matter' of DNA

Jan 18, 2013

In each cell, thousands of regulatory regions control which genes are active at any time. Scientists at the Research Institute of Molecular Pathology (IMP) in Vienna have developed a method that reliably ...

Recommended for you

Japanese scientist resigns over stem cell scandal

15 hours ago

A researcher embroiled in a fabrication scandal that has rocked Japan's scientific establishment said Friday she would resign after failing to reproduce results of what was once billed as a ground-breaking study on ...

'Hairclip' protein mechanism explained

Dec 18, 2014

Research led by the Teichmann group on the Wellcome Genome Campus has identified a fundamental mechanism for controlling protein function. Published in the journal Science, the discovery has wide-ranging implications for bi ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.