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.
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
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
Barbara Bachtler, | idw
Water forms 'spine of hydration' around DNA, group finds
26.05.2017 | Cornell University
How herpesviruses win the footrace against the immune system
26.05.2017 | Helmholtz-Zentrum für Infektionsforschung
Staphylococcus aureus is a feared pathogen (MRSA, multi-resistant S. aureus) due to frequent resistances against many antibiotics, especially in hospital infections. Researchers at the Paul-Ehrlich-Institut have identified immunological processes that prevent a successful immune response directed against the pathogenic agent. The delivery of bacterial proteins with RNA adjuvant or messenger RNA (mRNA) into immune cells allows the re-direction of the immune response towards an active defense against S. aureus. This could be of significant importance for the development of an effective vaccine. PLOS Pathogens has published these research results online on 25 May 2017.
Staphylococcus aureus (S. aureus) is a bacterium that colonizes by far more than half of the skin and the mucosa of adults, usually without causing infections....
Physicists from the University of Würzburg are capable of generating identical looking single light particles at the push of a button. Two new studies now demonstrate the potential this method holds.
The quantum computer has fuelled the imagination of scientists for decades: It is based on fundamentally different phenomena than a conventional computer....
An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.
We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...
Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.
Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...
An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...
24.05.2017 | Event News
23.05.2017 | Event News
22.05.2017 | Event News
26.05.2017 | Life Sciences
26.05.2017 | Life Sciences
26.05.2017 | Physics and Astronomy