The FANTOM, or Functional Annotation of the Mammalian cDNA, is a research consortium organized by RIKEN Omics Science Center (OSC) and made up of leading scientists in Australia, Switzerland, Norway, South Africa, Sweden, Canada, Denmark, Italy, Germany, Singapore, UK, and the United States.
The consortium has been providing the scientific community with extensive databases on the mammalian genome that describe molecular function, biology, and cell components. FANTOM is now a world authority on the mammalian transcriptome, the set of all messenger RNA, which shows active genetic expression at one point in time. Other major findings include the discovery that approximately 70% of the genome is transcribed, and that more than half of the expressed genes are likely non-coding RNAs (ncRNAs) that do not code proteins; thus, the prevalent idea that only 2% of the genome is transcribed into mRNA coding to proteins needed to be reexamined.
Now in its fourth stage, FANTOM4, led by OSC's Yoshihide Hayashizaki, has over 3 years of laborious research developed a novel technology for producing a genome-wide promoter expression profile, established a mathematical scheme for describing the data obtained, and extracted key genomic elements which play dominant roles in maintenance of cellular condition.
In the current research, OSC has broadened its original technology CAGE (Cap Analysis of Gene Expression) and created deepCAGE, which takes advantage of next-generation sequencing to both precisely identify transcription start sites genome-wide as well as to quantify the expression of each start site. The deepCAGE technology was applied to a differentiating acuye myeloid leukemia cell line (ACL) to provide genome-wide time course dynamics of expression at the level of individual promoters -- specific sequences on the DNA providing binding sites for RNA polymerase and the protein transcription factors that recruit them. The consortium built a quantitative model of the genome-wide gene expression dynamics which identified the key regulator motifs driving the differentiation, the time-dependent activities of the transcription regulators binding the motifs, and the genome-wide target promoters of each motif.
Validation of the model was performed by knocking down each transcription factor with small interfering RNAs. This first report of a large-scale gene network based on experimental data set is certain to generate a great deal of excitement in the scientific community. This information is also important for life science and medical researchers who are trying to uncover the processes by which cells undergo conversion or become cancerous, and for those attempting to determine how to control the growth and differentiation of stem cells and ensure their safety for use in regeneration medicine. Dr. Harukazu Suzuki, the scientific coordinator of the consortium, had this to say, "We are proud that we have created groundbreaking research in understanding more about how genes regulate cells at the molecular level and we want to acknowledge all consortium members for their great contribution to the research effort."
The FANTOM consortium has also expanded earlier discoveries of transcriptional complexity by exploring repetitive elements found throughout mammalian genomes with DeepCAGE,. These elements, which constitute up to half of the genome, have been generally considered to be junk or parasitic DNA. However, the team has found that the repetitive elements are broadly expressed and 6 to 30% of mouse and human mRNAs are derived from repetitive element promoters. These RNAs are often tissue-specific and dynamically controlled, and control the output of the genome through a variety of mechanisms. The FANTOM4 collaborators have also identified yet another type of short RNA, referred to as tiRNA (transcription initiation RNA) or tiny RNAs, in the human, chicken, and Drosphilia. They are about 18 nucleotides (nt) in length and are found within -60 to +120 nt of transcription start sites and may actually be widespread in metazoans (animals). A BioMed Central Thematic Series features even more FANTOM 4 research papers in Genome Biology and several BMC journals.
Contact:RIKEN Omics Science Center
Cordula Heinrich | idw
Further reports about: > Biology > CAGE > Cap Analysis of Gene Expression > DNA > FANTOM > FANTOM4 > International FANTOM consortium > OSC > RNA > Science TV > active genetic expression > cell components > deepCAGE technology > large-scale genome-wide data analysis > mammalian genome > molecular function > myeloid leukemia > non-coding RNAs > small interfering RNA > transcription factor > transcription initiation RNA
Drone vs. truck deliveries: Which create less carbon pollution?
31.05.2017 | University of Washington
New study: How does Europe become a leading player for software and IT services?
03.04.2017 | Fraunhofer-Institut für System- und Innovationsforschung (ISI)
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...
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...
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...
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...
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)...
19.06.2017 | Event News
13.06.2017 | Event News
13.06.2017 | Event News
26.06.2017 | Life Sciences
26.06.2017 | Physics and Astronomy
26.06.2017 | Information Technology