Navigation Links
New methods offer insight into regulatory DNA

Through the Human Genome Project, the HapMap Project and other efforts, we are beginning to identify genes that are modified in some diseases. More difficult to measure and identify are the regulatory regions in DNA ?the 'managers' of genes ?that control gene activity and might be important in causing disease.

Today, a team led by the Wellcome Trust Sanger Institute, together with colleagues in the USA and Switzerland, provide a measure of just how important regulatory region variation might be in a pilot study based on some 2% of the human genome. As many as 40 of 374 genes showed alteration in genetic activity that could be related to changes in DNA sequence called SNPs.

"We were amazed at the power of this study to detect associations between SNP variations and gene activity," commented Dr Manolis Dermitzakis, Investigator, Division of Informatics at the Wellcome Trust Sanger Institute. "We were even more amazed at the number of genes affected: more than 10% of our sample ?or perhaps 3000 genes across the genome ?could be subject to modification of activity in human populations due to common genetic variations."

The study combined the map of genetic variation developed through the HapMap with estimates of gene activity obtained from cell cultures from 60 individuals who provided samples for the HapMap. More than 630 genes were studied, of which 374 were active in the cell cultures. If gene activity in a cell culture was skewed from the average, it was investigated further.

These genes were correlated with more than 750,000 SNPs ?sequence differences between individuals in the sample collection. A series of statistical tests were carried out to provide increased confidence in the association between gene activity and sequence variation.

"Our sample size of 60 individuals is relatively small," continued Dr Dermitzakis, "and we might expect not to detect rare variations. However, our pilot project gives us greater confidence to take on a genome-wide survey of gene activity."

A global map of sequence variation and gene activity will be an important tool in the interpretation of variation and disease. Such genome-wide association studies will be able to identify some regions of the genome with strong disease effects.

"The HapMap is proving to be useful in a wide range of applications," commented Dr Panos Deloukas, Senior Investigator, Division of Medical Genetics, Wellcome Trust Sanger Institute. "The journey for our biomedical research is from DNA sequence to individual people and individual disease. The HapMap is a bridge from sequence data to the differences in individuals."

The project focused on three regions of the human genome. The first, called the ENCODE regions, and about 30 million base-pairs of DNA, are being intensively studied around the world as a group of 'typical' human genome regions. The second was 35million base-pairs of chromosome 21 sequence: three copies of chromosome 21 lead to Down Syndrome. The third was a region of chromosome 20 ?10 million base-pairs ?that is known to be associated with diabetes and obesity.

In comparison with gene sequences that contain the instructions to make proteins, regulatory regions that control genes are relatively poorly understood. Their structure is variable and their distance from the genes they control also varies among genes.

New tools are needed in the search of our genome for the sequences that contribute to disease, tools that will harness the massive amounts of DNA information and transform them into information of real biomedical utility. The methods described here, with the power of the HapMap data and the cell cultures available, will speed that transformation.


'"/>

Source:Public Library of Science


Related biology news :

1. Studies reveal methods viruses use to sidestep immune system
2. New methods of gene delivery using lasers
3. Shift of weather patterns necessitates rethinking of reforestation methods
4. Scientists use manufacturing methods to reconstruct mastodon
5. Researchers develop new testing methods for potential monkeypox or smallpox outbreak
6. Plant-derived molecules, genetic manipulation point to future chemoprevention methods
7. Application of Genomatix in silico methods reveals novel cancer associated genes
8. Ancient olfaction protein is shared by many bugs, offering new pest control target
9. Protein offers way to stop microscopic parasites in their tracks
10. Nanoparticles offer new hope for detection and treatment
11. Whats really making you sick? Plant pathologists offer the science behind Sick Building Syndrome
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:6/22/2016)... -- On Monday, the Department of Homeland Security (DHS) ... for the Biometric Exit Program. The Request for Information ... explains that CBP intends to add biometrics to confirm ... States , in order to deter visa overstays, ... Logo - http://photos.prnewswire.com/prnh/20160622/382209LOGO ...
(Date:6/20/2016)... 20, 2016 Securus Technologies, a leading ... for public safety, investigation, corrections and monitoring announced ... it has secured the final acceptance by all ... Managed Access Systems (MAS) installed. Furthermore, Securus will ... be installed by October, 2016. MAS distinguishes between ...
(Date:6/15/2016)... June 15, 2016 Transparency ... titled "Gesture Recognition Market by Application Market - Global Industry Analysis ... 2024". According to the report, the  global gesture recognition ... 2015 and is estimated to grow at a ... by 2024.  Increasing application of gesture ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... , June 23, 2016 Houston Methodist ... the Cy-Fair Sports Association to serve as their ... agreement, Houston Methodist Willowbrook will provide sponsorship support, ... connectivity with association coaches, volunteers, athletes and families. ... the Cy-Fair Sports Association and to bring Houston ...
(Date:6/23/2016)... ... June 23, 2016 , ... ... launch of the Supplyframe Design Lab . Located in Pasadena, Calif., the ... future of how hardware projects are designed, built and brought to market. , ...
(Date:6/23/2016)... June 23, 2016 ... 2016;12(1):22-8 http://doi.org/10.17925/OHR.2016.12.01.22 Published recently ... peer-reviewed journal from touchONCOLOGY, Andrew D Zelenetz ... of cancer care is placing an increasing burden ... expensive biologic therapies. With the patents on many ...
(Date:6/23/2016)... June 22, 2016  Amgen (NASDAQ: AMGN ... QB3@953 life sciences incubator to accelerate the ... shared laboratory space at QB3@953 was created to help ... obstacle for many early stage organizations - access to ... sponsorship, Amgen launched two "Amgen Golden Ticket" awards, providing ...
Breaking Biology Technology: