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:4/19/2016)... 2016 The new GEZE SecuLogic ... web-based "all-in-one" system solution for all door components. It ... the door interface with integration authorization management system, and ... The minimal dimensions of the access control and the ... installations offer considerable freedom of design with regard to ...
(Date:4/14/2016)... TEL AVIV, Israel , April 14, 2016 /PRNewswire/ ... in Behavioral Authentication and Malware Detection, today announced the ... has already assumed the new role. Goldwerger,s ... for BioCatch, on the heels of the deployment of ... In addition, BioCatch,s behavioral biometric technology, which discerns unique ...
(Date:3/31/2016)... , March 31, 2016  Genomics firm Nabsys has ... CEO, Barrett Bready , M.D., who returned to ... the original technical leadership team, including Chief Technology Officer, ... Product Development, Steve Nurnberg and Vice President of Software ... the company. Dr. Bready served as CEO ...
Breaking Biology News(10 mins):
(Date:5/26/2016)... 2016 Despite the volatility that continues ... space. Today,s pre-market research on ActiveWallSt.com directs the investor community,s ... RDUS ), Cerus Corp. (NASDAQ: CERS ... Five Prime Therapeutics Inc. (NASDAQ: FPRX ). Register ... http://www.activewallst.com/ On Wednesday, shares in ...
(Date:5/26/2016)... , ... May 26, 2016 , ... ... FireflySci cuvettes are used in leading laboratories all over the globe. Their cute ... In addition to manufacturing awesome cuvettes, FireflySci makes spectrophotometer calibration standards that never ...
(Date:5/25/2016)... ... May 25, 2016 , ... The Ankle Plating ... options designed to address fractures of the distal tibia and fibula. This system ... Ankle Plating System 3 is composed of seven plate families that span the ...
(Date:5/25/2016)... ... ... Scientists at the University of Athens say they have evidence that the variety ... that could lead to one good one. Surviving Mesothelioma has just posted an article ... team evaluated 98 mesothelioma patients who got a second kind of drug ...
Breaking Biology Technology: