Researchers Unlock the Secrets of Gene Regulatory Networks

February 4, 2009

A quartet of studies by researchers at the California Institute of Technology (Caltech) highlight a special feature on gene regulatory networks recently published in the Proceedings of the National Academy of Sciences (PNAS).

The collection of papers, "Gene Networks in Development and Evolution Special Feature, Sackler Colloquium," was coedited by Caltech's Eric H. Davidson, the Norman Chandler Professor of Cell Biology. His coeditor was Michael Levine, professor of genetics, genomics and development at the University of California, Berkeley.

"The control system that determines how development of an animal occurs in each species is encoded in the genome, and the physical location of the sequences where this code is resident is being revealed in a new area of systems biology--the study of gene regulatory networks," says Davidson. Gene regulatory networks are the complex networks of gene interactions that direct the development of any given species.

The papers in the collection focus on the gene regulatory networks of a variety of organisms, including fruit flies, soil-dwelling nematodes, sea urchins, lampreys, and mice.

"These networks lie at the heart of the regulatory apparatus, and they consist of genes that encode proteins that regulate other genes, and the DNA sequences which control when and where they are expressed," says Davidson, who authored a paper in the special feature about a gene regulatory network found in sea urchin embryos. He and Levine also coauthored a perspective in the same issue of the journal on the properties of gene regulatory networks.

In one paper, Ellen V. Rothenberg, one of the two Albert Billings Ruddock Professors of Biology at Caltech, examines, in mice, the intricate developmental pathway that causes blood stem cells to differentiate into T cells, a varied class of immune system cells that help the body fight off infection.

The paper, Rothenberg says, represents a "codification of everything we know about T cell development. We've found that getting the right balances of the various regulatory signals is absolutely crucial for the T cells to come out right. It gives one a sense of how subtle and sophisticated the regulation can be."

Another study in the special feature by Marianne Bronner-Fraser, the second Albert Billings Ruddock Professor of Biology, focuses on the gene regulatory network underlying neural crest formation in the lamprey, the most primitive living vertebrate. The neural crest is a group of embryonic cells that are pinched off during the formation of the neural tube--the precursor to the spinal cord--and then migrate throughout the developing body to form other nervous system structures.

The study "reveals order and linkages within the network at early stages," Bronner-Fraser says. "Because the neural crest cell type represents a vertebrate innovation, our work in lampreys shows that this network is ancient and tightly conserved to the base of vertebrates," she says.

The fourth of the Caltech papers, by Paul W. Sternberg, the Thomas Hunt Morgan Professor of Biology at Caltech and an investigator with the Howard Hughes Medical Institute (HHMI), and his colleagues, looks at a postembryonic gene regulatory network in Caenorhabditis elegans, a soil-dwelling worm commonly studied by developmental biologists. The gene regulatory network studied by Sternberg and his colleagues controls the formation of the worm's vulva, which connects the uterus with the outside and allows the passage of sperm and eggs.

All of the papers in the special feature arise out of presentations at a Sackler Colloquium held at the National Science Foundation's Beckman Center in Irvine, California, in February 2008.

Davidson's paper, "Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo," coauthored with Caltech postdoctoral scholar Joel Smith, was funded by the National Institutes of Health's (NIH) Institute of Child Health and Development and General Medical Sciences Institute and a California Institute of Regenerative Medicine (CIRM) fellowship to Smith.

Rothenberg's paper, "A gene regulatory network armature for T lymphocyte specification," represents a collaboration between Rothenberg and Hamid Bolouri, a visiting associate at Caltech, with support from the NIH, the Albert Billings Ruddock Professorship, the Louis A. Garfinkle Memorial Laboratory Fund, the Al Sherman Foundation, and the DNA Sequencer Royalty Fund. The paper was coauthored by Caltech senior postdoctoral research scholar Constantin Georgescu, and William Longabaugh of the Institute for Systems Biology in Seattle.

Bronner-Fraser's paper, "Gene regulatory networks in neural crest development and evolution," was coauthored by Caltech postdoctoral research scholars Natalya Nikitina and Tatjana Sauka-Spengler.

Sternberg's paper, "The Caenorhabditis elegans vulva: A post-embryonic gene regulatory network controlling organogenesis," was funded by the NIH and the HHMI.

Provided by Caltech

Explore further: Understanding Africa's diverse gene pool can help fight lifestyle diseases

Related Stories

How mammary glands appeared in the course of evolution

November 15, 2016

A joint team of geneticists from the University of Geneva (UNIGE) and the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, demonstrated that the emergence of mammary glands in placental mammals and marsupials ...

Changing cell behavior could boost biofuels, medicine

November 8, 2016

A computer scientist at Washington University in St. Louis has developed a way to coax cells to do natural things under unnatural circumstances, which could be useful for stem cell research, gene therapy and biofuel production.

Checkmate for Castleman disease

November 14, 2016

(Phys.org)—Dr. David Fajgenbaum is the founder of Castleman Disease Collaborative Network. Its goal is to organize patients with Castleman disease (CD), find an explanation for this rare and enigmatic immunological disorder ...

Sex, gender, or both in medical research

November 22, 2016

No one can deny that men and women have different genes, biology and anatomical features. However, only a minority of medical studies take this into account when analyzing and reporting research results. Time to hold researchers ...

Recommended for you

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.