Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Making sense of the genome

22.05.2003

Almost every week we hear of a new genome sequence being completed, yet turning sequence information into knowledge about what individual genes do is very difficult. An article published in Journal of Biology this week will simplify this task, as it describes a new online tool that dramatically improves predictions of how individual genes are regulated.

Dr. Wyeth Wasserman and his team have created this powerful new two-step method for identifying which regulators of gene expression, called transcription factors, are in control of individual genes. The new method is far more selective than its predecessors, reducing the number of biologically irrelevant transcription factors identified in a search by 85%. The researchers have now made the tool available through an easy to use website called ConSite.

This web-based tool will be particularly helpful in analysing genes whose coding sequences do not give any clues as to their function. Around 30% of the predicted human genes contain no recognisable domains. Through knowing which transcription factors control the expression of a particular gene, scientists can get an idea as to what processes the gene is involved in. This is because transcription factors are themselves tightly controlled to ensure that a gene is only expressed when and where it is needed, and a great deal is already known about which events activate which transcription factors.

"Knowledge of the identity of a mediating transcription factor can give important insights into the function of a gene," according to the authors of the article.

Transcription factors act by binding to specific sequences in a regulatory region that is located in the DNA upstream of the coding region. But they can tolerate a large amount of variation in these sequences. This means that searching an upstream regulatory region for transcription factor binding sites identifies a large number of such sites, most of which are biologically irrelevant.

The researchers successfully increased the signal to noise ratio of such searches by using a powerful combination of two methods. Firstly, the regulatory sequences are scanned for binding sites, but only for those that are known to be biologically active. For this comparison, Wasserman’s team compiled a searchable database of 108 transcription factor binding profiles from the relevant literature. The sites listed originate from mammals, insects and nematodes, and all are supported by good experimental evidence. These experiments provide essential information about the in vivo properties necessary for binding that are not contained in the sequence alone.

Secondly, the researchers use an alignment tool to compare the regulatory sequences of the same gene from two different species, and check which sites are conserved across evolution. "The most valuable information in the search for regulatory regions in genomic sequences is conservation. If a region is found to be conserved between a human genomic sequence and an orthologous genomic sequence from a distantly related organism, it is extremely likely to have a biological role," write the authors.

To test their two-step method, the researchers used it to identify the transcription factors that bind to the upstream regulatory regions of 14 well-studied genes. Using human and mouse sequences, the researchers found that all of the transcription factors identified did have a biological role and only a few of the physiologically relevant regulators were missed. A second test showed that the evolutionary distance between the two input sequences was vital in determining the effectiveness of the combined method.

This tool is now available to all scientists free of charge via the ConSite website: http://www.phylofoot.org/ Any scientist with a gene of interest will be able to input the regulatory sequence of their pet gene with or without the regulatory sequence of an orthologous gene into the ConSite tool, and will be rewarded with a list of probable regulators.

Gemma Bradley | BioMed Central
Further information:
http://jbiol.com/content/2/2/13
http://www.biomedcentral.com

More articles from Life Sciences:

nachricht Tiny probe that senses deep in the lung set to shed light on disease
17.06.2019 | University of Edinburgh

nachricht Exciting Plant Vacuoles
14.06.2019 | Julius-Maximilians-Universität Würzburg

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: MPSD team discovers light-induced ferroelectricity in strontium titanate

Light can be used not only to measure materials’ properties, but also to change them. Especially interesting are those cases in which the function of a material can be modified, such as its ability to conduct electricity or to store information in its magnetic state. A team led by Andrea Cavalleri from the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg used terahertz frequency light pulses to transform a non-ferroelectric material into a ferroelectric one.

Ferroelectricity is a state in which the constituent lattice “looks” in one specific direction, forming a macroscopic electrical polarisation. The ability to...

Im Focus: Determining the Earth’s gravity field more accurately than ever before

Researchers at TU Graz calculate the most accurate gravity field determination of the Earth using 1.16 billion satellite measurements. This yields valuable knowledge for climate research.

The Earth’s gravity fluctuates from place to place. Geodesists use this phenomenon to observe geodynamic and climatological processes. Using...

Im Focus: Tube anemone has the largest animal mitochondrial genome ever sequenced

Discovery by Brazilian and US researchers could change the classification of two species, which appear more akin to jellyfish than was thought.

The tube anemone Isarachnanthus nocturnus is only 15 cm long but has the largest mitochondrial genome of any animal sequenced to date, with 80,923 base pairs....

Im Focus: Tiny light box opens new doors into the nanoworld

Researchers at Chalmers University of Technology, Sweden, have discovered a completely new way of capturing, amplifying and linking light to matter at the nanolevel. Using a tiny box, built from stacked atomically thin material, they have succeeded in creating a type of feedback loop in which light and matter become one. The discovery, which was recently published in Nature Nanotechnology, opens up new possibilities in the world of nanophotonics.

Photonics is concerned with various means of using light. Fibre-optic communication is an example of photonics, as is the technology behind photodetectors and...

Im Focus: Cost-effective and individualized advanced electronic packaging in small batches now available

Fraunhofer IZM is joining the EUROPRACTICE IC Service platform. Together, the partners are making fan-out wafer level packaging (FOWLP) for electronic devices available and affordable even in small batches – and thus of interest to research institutes, universities, and SMEs. Costs can be significantly reduced by up to ten customers implementing individual fan-out wafer level packaging for their ICs or other components on a multi-project wafer. The target group includes any organization that does not produce in large quantities, but requires prototypes.

Research always means trying things out and daring to do new things. Research institutes, universities, and SMEs do not produce in large batches, but rather...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

SEMANTiCS 2019 brings together industry leaders and data scientists in Karlsruhe

29.04.2019 | Event News

Revered mathematicians and computer scientists converge with 200 young researchers in Heidelberg!

17.04.2019 | Event News

First dust conference in the Central Asian part of the earth’s dust belt

15.04.2019 | Event News

 
Latest News

A new paradigm of material identification based on graph theory

17.06.2019 | Materials Sciences

Electron beam strengthens recyclable nanocomposite

17.06.2019 | Materials Sciences

Tiny probe that senses deep in the lung set to shed light on disease

17.06.2019 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>