A cell’s RNA content provides a complete snapshot of its gene expression activity so can yield a bonanza of information not only about how that cell functions, but also the disruptions that result from disease or environmental changes.
The cap-analysis of gene expression (CAGE) technique developed by Piero Carninci and his colleagues at the RIKEN Omics Science Center in Yokohama has provided an invaluable tool for such profiling, enabling researchers to compile libraries of partial sequences from a large percentage of cellular RNAs1. However, CAGE requires large quantities of genetic material, limiting its usefulness for more focused cellular analyses. “We have been working with neurons, but there are so many types,” says Carninci. “If we isolate specific populations of fluorescently labeled transgenic neurons, we may obtain no more than several thousand cells.”
Working with an international team of collaborators, Carninci’s group has now developed two CAGE variants that bring such analyses within reach2. The first, nanoCAGE, can be applied to as little as ten nanograms of RNA—5,000-fold less than is needed for standard CAGE. Using nanoCAGE, the investigators could even selectively characterize RNAs from the nucleus, nucleolus and other cellular compartments.
Thanks to cellular splicing mechanisms, a single gene can yield multiple, functionally diverse gene products. However, CAGE and nanoCAGE only characterize the beginning of each RNA molecule, making it hard to identify splice variants. The second technique, CAGEscan, has therefore been adapted to yield sequence data from both ends, and initial demonstrations of this method on cultured liver cells enabled a detailed analysis of architecture and revealed a startling diversity of novel RNA molecules. Many of these arise from within non-protein-coding segments of known genes, and potentially exert yet-unknown regulatory functions.
These two techniques should enable a diverse array of genetics and cell biology studies that were not possible with traditional CAGE. “Analyzing isolated, homogeneous neuron populations from mice and rats is a high priority for us,” says Carninci. “These technologies could also be used on biopsies or samples, where the amount of RNA is generally limited or to look for diagnostic markers in the blood.”
Carninci and his colleagues are also thinking smaller, and attempting to focus their method all the way down to the single-cell level. “Scaling down the technology to a single cell will help solve the issue of how many cell types we have in the body,” he says, “and particularly in the brain, where this issue is especially debated.”
The corresponding author for this highlight is based at the Functional Genomic Technology Team, RIKEN Omics Science Center
1. Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., Kodzius, R., Watahiki, A., Nakamura, M., Arakawa, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proceedings of the National Academy of Sciences USA 100, 15776–15781 (2003).
2. Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, M., Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D. et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods 7, 528–534 (2010).
gro-pr | Research asia research news
Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München
Second research flight into zero gravity
21.10.2016 | Universität Zürich
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.
Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
21.10.2016 | Health and Medicine
21.10.2016 | Information Technology
21.10.2016 | Materials Sciences