Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

"Exciting new approach" for identifying microRNAs

09.04.2008
PhD student at MDC develops new computer program

MicroRNAs (miRNAs) are genes which produce important elements that regulate a wide variety of processes in plants, animals and humans. MiRNAs are considered to be promising diagnostic and therapeutic candidates for the treatment of human diseases. Worldwide, scientists are seeking to develop methods to detect which miRNAs are active in tissue samples or to identify novel miRNA genes.

To date, researchers have identified more than 600 human miRNAs, each of which regulates the activity of several hundred proteins, the building and operating materials of life. Marc Friedländer, a PhD student in the laboratory of Nikolaus Rajewsky at the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, Germany, has now developed a software package named miRDeep. Using it, researchers can detect not only which miRNAs are active in a tissue sample, but can also discover previously unknown miRNAs. MiRDeep is based on the analysis of modern high-throughput sequencing technologies and modeling the activity of a key enzyme in the miRNA pathway.

The paper, written in collaboration with Wei Chen of the Max Planck Institute (MPI) for Molecular Genetics, Berlin, has been published in Nature Biotechnology* online (Vol. 26, No. 4, pp. 407 - 415, 008). It also reports more than 250 novel or unannotated miRNA genes, 15 of these are human, which Friedländer and his colleagues were able to identify.

... more about:
»Molecular »RNA »Rajewsky »miRNA »produce »proteins

RNA is an abbreviation for ribonucleic acid. It is a chemical relative of DNA and functions as carrier of genetic information, which the cell needs to produce proteins. Besides this messenger RNA there are also miRNAs, small RNA fragments, which bind to certain regions of messenger RNA and thus block the production of proteins. MiRNA genes thus regulate which proteins the body generates.

Researchers want to utilize this process. "For instance, cancer researchers compare cancer cells with healthy cells to find out which miRNAs might play a role in the development of cancer," Rajewsky said, explaining the significance of miRNAs for basic medical research. "However, many known, but also still unknown miRNAs can only be found in small numbers in cells and are thus overlooked using traditional methods," he added. With novel "deep sequencing" methods, researchers can detect even these miRNAs. Using these revolutionary high-throughput sequencing technologies, genetic material can be decoded more rapidly and at lower cost.

Free access for researchers
"Until now," Rajewsky explained, "the problem also involved analyzing the immense amount of data generated by deep sequencing. Such a machine can easily decode 100 million letters of DNA in 3.5 days. Moreover, cells produce many other RNAs, not only miRNAs." Marc Friedländer developed the computer program "miRDeep".

Using this program, researchers can discover signatures in the sequencing data which are generated in the production of miRNAs in the cell. MiRDeep searches the data for these traces and then computes the probability with which a potential precursor-miRNA will produce a real miRNA. MiRDeep can be downloaded as software package from the website of the Rajewsky research group.

"Due to the good collaboration of bioinformaticians and lab biologists, we have succeeded in testing miRDeep in practice," Rajewsky said, describing the work of his research team. MDC researchers tested the new program by sequencing even small RNAs of human cancer cells and blood cells in the dog and analyzing these with miRDeep. They detected most of the already known miRNAs, but also 230 miRNAs that were previously unknown.

Various new miRNA genes could then also be validated by the researchers independently in the lab. "We started very early with the analysis of deep sequencing data and were thus able to gain experience, which is necessary considering the complexity and magnitude of the data." He summed up by saying, "Generally, until now there have been very few published methods for analyzing this data. Right now we are just at the beginning of this exciting research."

*miRDeep: Discovering miRNAs from deep sequencing data

Marc R. Friedländer1, Wei Chen2, Catherine Adamidi1 , Jonas Maaskola1, Ralf Einspanier3, Signe Knespel1, and Nikolaus Rajewsky1,*

1 Max Delbrück Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany
2 Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany
3 Institute of Veterinary Biochemistry, Freie Universität Berlin, Oertzenweg 19b, D-14163 Berlin, Germany

doi:10.1038/nbt1394

Barbara Bachtler
Press and Public Affairs
Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch
Robert-Rössle-Straße 10; 13125 Berlin; Germany
Phone: +49 (0) 30 94 06 - 38 96
Fax: +49 (0) 30 94 06 - 38 33
e-mail: presse@mdc-berlin.de
http://www.mdc-berlin.de/en/news

Barbara Bachtler, | idw
Further information:
http://en.wikipedia.org/wiki/DNA_sequencing
http://en.wikipedia.org/wiki/RNA_interference
http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/index.html

Further reports about: Molecular RNA Rajewsky miRNA produce proteins

More articles from Life Sciences:

nachricht Cell Division at High Speed
19.06.2019 | Julius-Maximilians-Universität Würzburg

nachricht Monitoring biodiversity with sound: how machines can enrich our knowledge
18.06.2019 | Georg-August-Universität Göttingen

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Successfully Tested in Praxis: Bidirectional Sensor Technology Optimizes Laser Material Deposition

The quality of additively manufactured components depends not only on the manufacturing process, but also on the inline process control. The process control ensures a reliable coating process because it detects deviations from the target geometry immediately. At LASER World of PHOTONICS 2019, the Fraunhofer Institute for Laser Technology ILT will be demonstrating how well bi-directional sensor technology can already be used for Laser Material Deposition (LMD) in combination with commercial optics at booth A2.431.

Fraunhofer ILT has been developing optical sensor technology specifically for production measurement technology for around 10 years. In particular, its »bd-1«...

Im Focus: The hidden structure of the periodic system

The well-known representation of chemical elements is just one example of how objects can be arranged and classified

The periodic table of elements that most chemistry books depict is only one special case. This tabular overview of the chemical elements, which goes back to...

Im Focus: MPSD team discovers light-induced ferroelectricity in strontium titanate

Light can be used not only to measure materials’ properties, but also to change them. Especially interesting are those cases in which the function of a material can be modified, such as its ability to conduct electricity or to store information in its magnetic state. A team led by Andrea Cavalleri from the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg used terahertz frequency light pulses to transform a non-ferroelectric material into a ferroelectric one.

Ferroelectricity is a state in which the constituent lattice “looks” in one specific direction, forming a macroscopic electrical polarisation. The ability to...

Im Focus: Determining the Earth’s gravity field more accurately than ever before

Researchers at TU Graz calculate the most accurate gravity field determination of the Earth using 1.16 billion satellite measurements. This yields valuable knowledge for climate research.

The Earth’s gravity fluctuates from place to place. Geodesists use this phenomenon to observe geodynamic and climatological processes. Using...

Im Focus: Tube anemone has the largest animal mitochondrial genome ever sequenced

Discovery by Brazilian and US researchers could change the classification of two species, which appear more akin to jellyfish than was thought.

The tube anemone Isarachnanthus nocturnus is only 15 cm long but has the largest mitochondrial genome of any animal sequenced to date, with 80,923 base pairs....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

SEMANTiCS 2019 brings together industry leaders and data scientists in Karlsruhe

29.04.2019 | Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

First dust conference in the Central Asian part of the earth’s dust belt

15.04.2019 | Event News

 
Latest News

A new force for optical tweezers awakens

19.06.2019 | Physics and Astronomy

New AI system manages road infrastructure via Google Street View

19.06.2019 | Information Technology

A new manufacturing process for aluminum alloys

19.06.2019 | Materials Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>