Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Deciphering the regulatory code

05.11.2009
EMBL scientists take new approach to predict gene expression

Embryonic development is like a well-organised building project, with the embryo’s DNA serving as the blueprint from which all construction details are derived.

Cells carry out different functions according to a developmental plan, by expressing, i.e. turning on, different combinations of genes. These patterns of gene expression are controlled by transcription factors: molecules which bind to stretches of DNA called cis-regulatory modules (CRMs), and, once bound, switch the relevant genes on or off.

Thanks to scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, it is now possible to accurately predict when and where different CRMs will be active. The study, published today in Nature, is a first step towards forecasting the expression of all genes in a given organism and demonstrates that the genetic regulation that is crucial for correct embryonic development is more flexible than previously thought.

Through an interdisciplinary collaboration between biologist Robert P. Zinzen, computer scientist Charles Girardot and statistician Julien Gagneur, a novel, integrated approach was possible. They combined detailed experimental data about where and when transcription factors are binding to CRMs with a computational approach, and were able to forecast CRM activity.

“Going from global binding data to CRM activity was a big challenge in the field – one which we have now begun to overcome”, says Eileen Furlong, who headed the study.

Using a comprehensive, systematic approach, the scientists identified and recorded the binding profiles – i.e. the combinations of transcription factors binding at different times and places – of approximately 8000 CRMs involved in regulating muscle development in the fruit fly Drosophila. The activity of a number of such CRMs had been previously studied, and the EMBL team used this information to group them into classes according to the type of muscle and developmental stages they were active in. The scientists then trained a computer to unravel the binding profiles for each of these groups, and search the 8000 newly identified CRMs for ones whose binding profiles fitted that picture. Such CRMs were predicted to have similar activity patterns, implying they are involved in regulating the development of the same muscle type.

When the scientists tested their predictions experimentally, the results were not only accurate but also enlightening. It turns out that the regulatory code, in which one binding profile leads to one pattern of CRM activity, is actually not that straightforward. CRMs with strikingly different binding profiles can have similar patterns of activity. This plasticity was unexpected, but makes sense in evolutionary terms, the researchers say. The fact that different combinations of transcription factors, or binding codes, can regulate the same developmental process means that even if some transcription factors or CRMs change or are lost during an organism’s evolution, it can still develop a gut muscle, for instance.

“What’s exciting for me is that this study shows that it is possible to predict when and where genes are expressed, which is a crucial first step towards understanding how regulatory networks drive development”, Furlong concludes.

Sonia Furtado | EMBL Press Office
Further information:
http://www.embl.de
http://www.embl.de/aboutus/communication_outreach/media_relations/2009/091104_Heidelberg/index.html

More articles from Life Sciences:

nachricht Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden

nachricht The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: The pyrenoid is a carbon-fixing liquid droplet

Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.

A warming planet

Im Focus: Highly precise wiring in the Cerebral Cortex

Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.

The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Rainbow colors reveal cell history: Uncovering β-cell heterogeneity

22.09.2017 | Life Sciences

Penn first in world to treat patient with new radiation technology

22.09.2017 | Medical Engineering

Calculating quietness

22.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>