Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

RIKEN chooses Helicos single molecule sequencing for global map of human promoters

08.12.2010
Researchers in Japan have launched FANTOM5, Functional Annotation of the Mammalian Genome, an international effort to globally map transcription initiation in every human cell type.

Researchers in Japan have launched FANTOM5, Functional Annotation of the Mammalian Genome, an international effort to globally map transcription initiation in every human cell type.

Joint research by RIKEN and Helicos BioSciences Corporation has played a key role in this project in adapting the Cap Analysis of Gene Expression (CAGE) technique, originally developed by RIKEN, to the HeliscopeTM single molecule sequencer. The use of HeliscopeTM for CAGE completely avoids PCR amplification biases, is quantitative over 5 orders of magnitude, is highly reproducible and can be carried out on as little as 100ng of total RNA.

The FANTOM project is the brainchild of Yoshihide Hayashizaki, who launched the first phase of the project in 2000. The cDNA encyclopedia of mouse full-length cDNAs generated in the FANTOM1, 2 and 3 projects remains to this day the largest collection of mammalian full-length cDNAs. FANTOM3 provided insights into non-coding RNAs and sense-antisense regulation. It also introduced the CAGE technique, developed by Piero Carninci, which generates sequence tags from the 5’ ends of capped RNAs.

In FANTOM4, CAGE was applied to an acute myeloid leukemia cell line undergoing monocytic differentiation. Using CAGE and transcription factor binding site predictions, a transcriptional regulatory model was generated which identified the key transcription factors involved in monocytic differentiation. FANTOM5 takes this one huge leap further by trying to generate transcriptional regulatory models to define every human cell type.

Motivating the project is the idea that to build a full understanding of transcriptional regulation in a human system, we need to collect as large a set of diverse cellular states as possible. Different cellular states will express different subsets of genes, which in turn must be regulated by different combinations of transcription factors. While a large collection of human primary cell types has already been amassed for the project, many more are still needed. Potential collaborators working on rare cell types are invited to contact Alistair Forrest, who is co-coordinating sample collection for the project.

For more information, please contact:
Dr. Yoshihide Hayashizaki
Director, RIKEN Omics Science Center
General Organizer, FANTOM5 Project
The FANTOM5 headquarter:
Alistair Forrest, Jun Kawai, Piero Carninci, Hideya Kawaji, Carsten Daub, Harukazu Suzuki
RIKEN Omics Science Center
TEL: +81-45-503-9222 FAX: +81-45-503-9216
Email: fantom5_enquiries@gsc.riken.jp
About RIKEN
RIKEN is a Japanese research institute that carries out high-level experimental and research work in a wide range of fields, including physics, chemistry, medical science, biology, and engineering, covering the entire range from basic research to practical applications. RIKEN was first organized in 1917 as a private research foundation and was reorganized in 2003 as an independent administrative institution under the Ministry of Education, Culture, Sports, Science and Technology.

RIKEN Omics Science Center is one of 12 research centers in RIKEN and its focus is on developing genome-wide technologies and applications thereof.

gro-pr | Research asia research news
Further information:
http://www.osc.riken.jp/english/
http://www.researchsea.com

More articles from Life Sciences:

nachricht Zap! Graphene is bad news for bacteria
23.05.2017 | Rice University

nachricht Discovery of an alga's 'dictionary of genes' could lead to advances in biofuels, medicine
23.05.2017 | University of California - Los Angeles

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Turmoil in sluggish electrons’ existence

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...

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

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...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

Im Focus: Bacteria harness the lotus effect to protect themselves

Biofilms: Researchers find the causes of water-repelling properties

Dental plaque and the viscous brown slime in drainpipes are two familiar examples of bacterial biofilms. Removing such bacterial depositions from surfaces is...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

AWK Aachen Machine Tool Colloquium 2017: Internet of Production for Agile Enterprises

23.05.2017 | Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

Innovation 4.0: Shaping a humane fourth industrial revolution

17.05.2017 | Event News

 
Latest News

Zap! Graphene is bad news for bacteria

23.05.2017 | Life Sciences

Medical gamma-ray camera is now palm-sized

23.05.2017 | Medical Engineering

Discovery of an alga's 'dictionary of genes' could lead to advances in biofuels, medicine

23.05.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>