Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Intercepted messages reveal cells' inner workings

23.08.2010
A pair of molecular biology techniques enables detailed characterization of the gene expression of small numbers of cells

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
Further information:
http://www.rikenresearch.riken.jp/eng/research/6374
http://www.researchsea.com

Further reports about: CAGE CAGEscan Omics RIKEN RNA RNA molecule Science TV cell type environmental change

More articles from Life Sciences:

nachricht For a chimpanzee, one good turn deserves another
27.06.2017 | Max-Planck-Institut für Mathematik in den Naturwissenschaften (MPIMIS)

nachricht New method to rapidly map the 'social networks' of proteins
27.06.2017 | Salk Institute

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Touch Displays WAY-AX and WAY-DX by WayCon

27.06.2017 | Power and Electrical Engineering

Drones that drive

27.06.2017 | Information Technology

Ultra-compact phase modulators based on graphene plasmons

27.06.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>