Satellite Banner
Genomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

More Functional DNA in Genome than Previously Thought

Published: Thursday, December 20, 2007
Last Updated: Thursday, December 20, 2007
Bookmark and Share
Hopkins researchers report that non-coding DNA, that contributes to inherited diseases like Parkinson’s or mental disorders, may be more abundant than we realize.

Surrounding the small islands of genes within the human genome is a vast sea of mysterious DNA. While most of this non-coding DNA is junk, some of it is used to help genes turn on and off.

As reported online this week in Genome Research, Hopkins researchers have now found that this latter portion, which is known as regulatory DNA and contributes to inherited diseases like Parkinson’s or mental disorders, may be more abundant than we realize.

By conducting an exhaustive analysis of the DNA sequence around a gene required for neuronal development, Andrew McCallion, Ph.D., an assistant professor in the McKusick-Nathans Institute of Genetic Medicine, and his team found that current computer programs that scan the genome looking for regulatory DNA can miss more than 60 percent of these important DNA regions.

The current methods find regulatory sequences by comparing DNA from distantly related species, under the theory that functionally important regions will appear more similar in sequence than non-functional regions. “The problem with this approach, we have discovered,” says McCallion, “is that it’s often throwing the baby out with the bath water. So while we believe sequence conservation is a good method to begin finding regulatory elements, to fully understand our genome we need other approaches to find the missing regulatory elements.”

McCallion had suspected that using sequence conservation would overlook some regulatory DNA, but to see how much, he set up a small pilot project looking at the phox2b gene; he chose this gene both because of its small size and his interest in nerve development (phox2b is involved in forming part of the brain associated with stress response as well as nerves that control the digestive system).

The researchers created what they call a “tiled path,” cutting up the DNA sequence around the phox2b gene into small pieces, then inserted each piece into zebrafish embryos along with a gene for a fluorescent protein. If a phox2b fragment was a regulatory element, then it would cause the protein to glow. By watching the growing fish embryos - which have the advantage of being transparent - the researchers could see which pieces were regulators.

They uncovered a total of 17 discrete DNA segments that had the ability to make fish glow in the right cells. The team then analyzed the entire region around the phox2b gene using the five commonly used computer programs that compute sequence conservation; these established methods picked up only 29 percent to 61 percent of the phox2b regulators McCallion identified in the zebrafish experiments.

“Our data supports the recent NIH encyclopedia of DNA elements project, which suggests that many DNA sequences that bind to regulatory proteins are in fact not conserved,” says McCallion. “I hope this pilot shows that these types of analyses can be worthwhile, especially now that they can be done quickly and easily in zebrafish.”

McCallion is now planning a larger study of other neuronal genes. “I think we are only starting to realize the importance and abundance of regulatory elements; by regulating the gene activity in each cell they help create the diverse range of cell types in our body.”

The research was funded by the National Institutes of Health and the March of Dimes.

Authors on the paper are David McGaughey, Ryan Vinton, Jimmy Huynh, Amr Al-Saif, Michael Beer and McCallion of Johns Hopkins.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,500+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Tumor-Only Genetic Sequencing May Misguide Cancer Treatment in Nearly Half of All Patients
Johns Hopkins scientists say the genetic code of tumors must be compared to patients’ noncancer genome to get a true picture.
Thursday, April 16, 2015
New Genetic and Epigenetic Contributors to Diabetes Identified
Comparison of fat cells in mice and men hints at how genes and environment conspire to produce disease.
Wednesday, January 07, 2015
When DNA Gets Sent to Time-Out
New details revealed in the coordinated regulation of large stretches of DNA.
Tuesday, January 06, 2015
CRISPR Shows Promise in Engineering Human Stem Cells
Johns Hopkins study could advance use of stem cells for treatment and disease research.
Monday, January 05, 2015
Up-close Look at Cancer on the Move
Microscopic view of metastasis could give insight about how to keep cancer in check.
Friday, November 07, 2014
Potential New 'Twist' in Breast Cancer Detection
Mouse studies reveal new and better picture of stem cells that may fuel some breast cancers.
Monday, December 07, 2009
Johns Hopkins Researchers Develop Human Stem Cell Line Containing Sickle Cell Anemia Mutation
Researchers establish a human cell-based system for studying the disease by reprogramming somatic cells to an embryonic stem cell like state.
Tuesday, June 03, 2008
Johns Hopkins Researcher Leads International Effort to Create “Proteinpedia”
A Johns Hopkins researcher has led the effort to compile to date the largest free resource of experimental information about human proteins.
Thursday, February 07, 2008
RNA Shown to Silence Cancer Suppressor Gene
Discovery sheds light on epigenetic mechanisms in tumor development in plants and animals.
Tuesday, January 15, 2008
Cellular Pump Sabotages Cancer Drug Studies that use Glow Chemical
Scientists discover that a widely used means of illuminating cancer cells could undermine studies of the potential value of experimental anti-cancer drugs.
Thursday, January 03, 2008
Omicia and Johns Hopkins Receive Small Business Technology Transfer Grant from NIH
Omicia recieves a $187,700 grant from NIH to support a collaboration with Johns Hopkins University to identify genetic causes of cardiovascular disease.
Friday, August 17, 2007
Key to Lung Cancer Chemo Resistance Revealed
Products made by a gene called NRF2 normally protect cells from environmental pollutants.
Tuesday, October 17, 2006
Scientific News
Liquid Biopsies: Utilization of Circulating Biomarkers for Minimally Invasive Diagnostics Development
Market Trends in Biofluid-based Liquid Biopsies: Deploying Circulating Biomarkers in the Clinic. Enal Razvi, Ph.D., Managing Director, Select Biosciences, Inc.
Genetic Tug of War
Researchers have reported on a version of genetic parental control in mice that is more targeted, and subtle than canonical imprinting.
Error Correction Mechanism in Cell Division
Cell biologists have reported an advance in understanding the workings of an error correction mechanism that helps cells detect and correct mistakes in cell division early enough to prevent chromosome mis-segregation and aneuploidy, that is, having too many or too few chromosomes.
How to Become a Follicular T Helper Cell
Uncovering the signals that govern the fate of T helper cells is a big step toward improved vaccine design.
Researchers Resurrect Ancient Viruses
Researchers at Massachusetts Eye and Ear and Schepens Eye Research Institute have reconstructed an ancient virus that is highly effective at delivering gene therapies to the liver, muscle, and retina.
Cell Aging Slowed by Putting Brakes on Noisy Transcription
Experiments in yeast hint at ways to extend life of some human cells.
Long Telomeres Associated with Increased Lung Cancer Risk
Genetic predisposition for long telomeres predicts increased lung adenocarcinoma risk.
Expanding the Brain
A team of researchers has identified more than 40 new “imprinted” genes, in which either the maternal or paternal copy of a gene is expressed while the other is silenced.
Identifying a Key Growth Factor in Cell Proliferation
Researchers discover that aspartate is a limiter of cell proliferation.
Study Uncovers Target for Preventing Huntington’s Disease
Scientists from Cardiff University believe that a treatment to prevent or delay the symptoms of Huntington’s disease could now be much closer, following a major breakthrough.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!