DNA arrays decipher genome's master switches

December 20, 2000

New DNA Array Method Helps Researchers Decipher Genome's Master Switches

Researchers at the Whitehead Institute and Corning Inc. have invented a powerful new microarray technique that can decipher the function of master switches in a cell by identifying the circuit, or the set of genes, they control across the entire genome. The researchers show that the technique can correctly identify the circuits controlled by two known master switches in yeast. In addition, the technique allows researchers to unravel in a week what takes years to achieve by conventional methods.

"We are very excited by these results because they suggest that our technique can be used to create a "user's manual" for the cell's master controls, a booklet that matches the master switches to the circuits they control in the genome," says Whitehead Member Richard Young who led the study.

The technique, published in the December 22 issue of Science, also provides researchers new scientific muscle needed to piece together the master wiring diagram--the controls and the circuits--that operate the complicated machinery of life.

Creating such a diagram represents the next step toward using the information from the Human Genome Project. For although the Human Genome Project will soon provide researchers a catalog of all the genes that make up a human being, it will in many ways be analogous to having the complete parts list for a Boeing 777, say researchers. The information does not tell us anything about putting all the parts together, nor does it tell us how the cockpit controls function to make the plane fly.

"Our technique creates the documentation needed to put the parts together and identifies how the major controls are connected to these parts," says Young. Such information will be fundamental to finding the genetic basis of diseases and for discovering better drugs.

The technique also will help solve many unanswered questions in cancer research, says Young. Malfunctioning of master switches have been shown to lead to cancer, but little is known about the nature of the circuitry they control.

The genome's master switches are DNA-binding proteins called gene activators. In humans, there are about a 1000 such activators controlling important functions in life, including cell growth and development. Some of the best known of these switches--the p53 protein, for example--are those that play a role in cancer. Others play a role during development, designating which cells become nerve or muscle cells, for instance. Scientists know the identity of nearly 600 master switches and know the function of at least 250 of them; their hope always has been to find the set of all genes they control so that they could crack open the genetic basis of health and disease.

However, finding all the genes--i.e., the circuitry--directly controlled by any given master switch has been a painstakingly long and tedious process, involving years of biochemical and molecular experiments. The new technique reported in Science provides a way to get the data in a global fashion and will allow researchers to do in a week what would have taken years to achieve.

"Our technique could conceivably be used in human cells to create a map matching up the master switches with the circuits they control," says Bing Ren, a postdoc in the Young lab.

Although DNA arrays are useful in determining a cell's expression profile (a snapshot of which genes are turned on and off in a cell) they represent an overall picture and capture the cell's state at a moment in time. One perturbation in the environment or a slight change in the tumor could trigger a cascade of changes, all of which are captured in the snapshot. Such information is invaluable to researchers, but when it comes to identifying the one crucial master switch, finding it from DNA arrays can be like finding a needle in the haystack.

In this study, the Young lab scientists created a technique to overcome this problem. The technique involves first fixing DNA-binding proteins in living cells to their binding sites using chemical crosslinking methods and then breaking open the cells to create a molecular soup of DNA-protein complexes. Specific antibodies coupled with magnetic beads are then used to fish out DNA fragments cross-linked to proteins of interest. This provides researchers a pure population of DNA-protein complexes, and unhooking the cross-linked DNA from the protein leaves them with DNA fragments that bind to proteins of interest. The researchers then label these fragments with fluorescent dye and hybridize them to a DNA array containing genomic DNA from yeast to reveal their identity.

"Our goal is to use this technique to find the circuits controlled by the 200 or so master switches in yeast and then develop analogous techniques in humans," says Young.
-end-
This work was supported by funds from Corning Inc., National Institutes of Health, Helen Hay Whitney Foundation, National Cancer Institute of Canada, National Science Foundation, Howard Hughes Medical Institute, European Molecular Biology Organization, and the Human Frontier Science Foundation.

For more information call
Seema Kumar or Nadia Halim
at 617-258-7270
kumar@wi.mit.edu
http://www.wi.mit.edu


Whitehead Institute for Biomedical Research

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.