Featured Research

from universities, journals, and other organizations

Gene Regulators Bind Promiscuously, But Often Do Nothing

Date:
February 12, 2008
Source:
PLoS Biology
Summary:
ChIP/chip analysis indicates that sequence-specific transcription factors bind to overlapping sets of thousands of genomic regions in Drosophila embryos, but most regions are bound at low levels and many may not be functional targets of these factors.

ChIP/chip analysis indicates that sequence-specific transcription factors bind to overlapping sets of thousands of genomic regions in Drosophila embryos, but most regions are bound at low levels and many may not be functional targets of these factors. Biologists are developing ever more sophisticated means to characterize molecular interactions in living systems. But a new study suggests that many of the interactions detected by a widely-used experimental method are functionally irrelevant.

ChIP-chip is a "hot technique" in biology, allowing scientists to visualize the binding between regulatory proteins and genes and thereby investigate the mechanisms and controls that operate as an organism develops from a fertilized egg to a complicated adult. However, a new study shows that there are many more of these binding events than expected and that most of them appear not to be involved in gene expression.

The fruit fly is an important model for the study of development, the process by which embryonic cells are able to multiply and form three-dimensional structures that eventually become tissues, organs and finally entire organisms. The blueprints for this transformation are encoded in the genes of every cell, and are "read out" by vast networks of regulatory proteins called transcription factors, which determine where and when genes are expressed.

It has been generally assumed that transcription factors are targeted to a limited set of genes and that they regulate expression wherever they are bound. However, a team of researchers from the Lawrence Berkeley National Lab and the University of California at Berkeley, led by Mark Biggin and Michael Eisen, found that there are thousands of regions reproducibly bound by each factor. "This is several orders of magnitude more genes than these factors are thought to regulate," said Eisen, "raising the question of what the function of the binding is."

Rather than simply classify regions as bound or unbound, as other researchers have done, the Berkeley team examined the full scope of binding observed in their ChIP-chip data and focused on differences in the amount of factor bound to each gene. They found a clear relationship between the number of factor molecules bound at a given site, and the site's role in gene regulation; DNA sites that bound the most molecules were those already thought to be key to the regulation during development. Much of the low level binding detected at thousands of genes, while clearly representing real molecular interactions, appears to play no role in regulating gene expression.

Based on their observations, the Berkeley Lab researchers argue that many of the regulatory connections proposed in earlier studies are likely to be incorrect. "Realizing that much of the binding detected in these assays may be non-functional significantly impacts how the results of these experiments should be interpreted," said Biggin. "The analysis and conclusions of published ChIP-chip studies should be reexamined with this possibility in mind."

Citation: Li X, MacArthur S, Bourgon R, Nix D, Pollard DA, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6(2): e27. doi:10.1371/journal.pbio.0060027


Story Source:

The above story is based on materials provided by PLoS Biology. Note: Materials may be edited for content and length.


Cite This Page:

PLoS Biology. "Gene Regulators Bind Promiscuously, But Often Do Nothing." ScienceDaily. ScienceDaily, 12 February 2008. <www.sciencedaily.com/releases/2008/02/080212085839.htm>.
PLoS Biology. (2008, February 12). Gene Regulators Bind Promiscuously, But Often Do Nothing. ScienceDaily. Retrieved September 19, 2014 from www.sciencedaily.com/releases/2008/02/080212085839.htm
PLoS Biology. "Gene Regulators Bind Promiscuously, But Often Do Nothing." ScienceDaily. www.sciencedaily.com/releases/2008/02/080212085839.htm (accessed September 19, 2014).

Share This



More Health & Medicine News

Friday, September 19, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

The Cost of Ebola

The Cost of Ebola

Reuters - Business Video Online (Sep. 18, 2014) As Sierra Leone prepares for a three-day "lockdown" in its latest bid to stem the spread of Ebola, Ciara Lee looks at the financial implications of fighting the largest ever outbreak of the disease. Video provided by Reuters
Powered by NewsLook.com
What HealthKit Bug Means For Your iOS Fitness Apps

What HealthKit Bug Means For Your iOS Fitness Apps

Newsy (Sep. 18, 2014) Apple has delayed the launch of the HealthKit app platform, citing a bug. Video provided by Newsy
Powered by NewsLook.com
U.S. Food Makers Surpass Calorie-Cutting Pledge

U.S. Food Makers Surpass Calorie-Cutting Pledge

Newsy (Sep. 18, 2014) Sixteen large food and beverage companies in the United States that committed to cut calories in their products far surpassed their target. Video provided by Newsy
Powered by NewsLook.com
Residents Vaccinated as Haiti Fights Cholera Epidemic

Residents Vaccinated as Haiti Fights Cholera Epidemic

AFP (Sep. 18, 2014) Haitians receive the second dose of the vaccine against cholera as part of the UN's vaccination campaign. Duration: 00:34 Video provided by AFP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins