Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

International FANTOM consortium publishes three millstone papers based on large-scale genome-wide data analysis

22.04.2009
The international FANTOM consortium announces publication of three milestone papers in the prestigious journal Nature Genetics that will challenge current notions of how genes are controlled in mammals.

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
Director Yoshihide Hayashizaki
Project director Harukazu Suzuki
TEL: +81-45-503-2222 FAX: +81-45-503-9216
Public Relations Office
Keiko Iwano
TEL: +81-48-467-9272 FAX: +81-48-462-4715

Cordula Heinrich | idw
Further information:
http://fantom.gsc.riken.jp/
http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.375.html

More articles from Studies and Analyses:

nachricht Europe’s Demographic Future. Where the Regions Are Heading after a Decade of Crises
10.08.2017 | Berlin-Institut für Bevölkerung und Entwicklung

nachricht Scientists reveal source of human heartbeat in 3-D
07.08.2017 | University of Manchester

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

Cholesterol-lowering drugs may fight infectious disease

22.08.2017 | Health and Medicine

Meter-sized single-crystal graphene growth becomes possible

22.08.2017 | Materials Sciences

Repairing damaged hearts with self-healing heart cells

22.08.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>