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Evolution of Human Genome's 'Guardian' Network

By  Mike Resnick and the Cincinnati Children's Hospital Medical Center
February 2008

Research Geneticist and lead author Michael Resnick
Research Geneticist and lead author Michael Resnick (Photo courtesy of Steve McCaw)
Research Fellow Daniel Menendez
Research Fellow Daniel Menendez (Photo courtesy of Steve McCaw)
Former NIEHS Research Fellow Alberto Inga, Ph.D.
Former NIEHS Research Fellow Alberto Inga, Ph.D. (Photo courtesy of Steve McCaw)

Human evolution has created enhancements in key genes connected to the p53 regulatory network -- the so-called guardian of the genome -- that boost the network's safeguards against DNA damage that could cause cancer or a variety of genetic diseases, according to  an international team of scientists led by the National Institute of Environmental Health Sciences (NIEHS) that included Cincinnati Children's Hospital Medical Center. Their study, titled "Functional Evolution of the p53 Regulatory Network through Its Target Response Elements," Exit NIEHS Website( appeared in the Jan. 22 Proceedings of the National Academy of Sciences (PNAS). Because genetically engineered mouse models are increasingly powerful tools in understanding the risks and mechanisms of human diseases, and rodents do not have the same evolution-based safeguards in p53 function as humans, the study also underscores the need for additional considerations in the interpretation of research using rodent models.

"Our findings are especially important because rodents are often used as model organisms to investigate the genetic origins of diseases that affect humans, as in research by cancer investigators evaluating the impact of DNA-damaging agents," said Anil Jegga, D.V.M, a researcher in the Division of Biomedical Informatics at Cincinnati Children's and key contributor to the study. "Rodent models remain important to our understanding of disease processes, although our study suggests the need to address experimentally the differences in p53 regulatory pathways between humans and rodent models."

"The findings reveal a new piece of the p53 puzzle and help us to understand how genes became part of the network," suggested Michael A. Resnick, Ph.D., who led the study and is head of the Chromosome Biology Group at NIEHS. Resnick and his team have been characterizing the functions of p53, a well-known suppressor of tumors, and have created systems in mouse, human and yeast cells that address contributions of normal and tumor mutant p53 in regulation of genes. The functional models, concepts and rules developed in Resnick's lab, previously described in PNAS in terms of a hand playing a piano, provided a conceptual base for launching the study.

The comparative functional genomics aspect of the study was driven by Jegga and his colleagues who looked systematically at small DNA sequences associated with the promoters, or enhancers, of specific genes that carry out orders from p53. These promoter elements act like antennae -- responding to activated p53 by boosting target gene expression and function inside a cell's nucleus. Using the functional rules and comparing the response element sequences across nearly 50 different binding sites of genes in the p53 network within 14 species (from zebra fish to humans), the researchers were able to reveal critical evolutionary changes in the function of genes involved in the repair of DNA damage.

The 14 species represented an estimated 500 million years of evolutionary separation, helping investigators determine how the function of p53 response elements was conserved or changed as different species developed. Jegga said researchers were surprised to find the acquisition of functional response for certain genes involved in DNA metabolism or repair to be mostly unique in humans. While the p53 functional responsiveness of many genes is shared with chimpanzees and rhesus monkeys, researchers said the p53 control of DNA metabolism and repair functions is lacking in rodents.

In humans, when DNA damage is detected, the p53 network seems to have gained additional capabilities that allow it to slow cell growth, initiate repairs or, if needed, apoptotic cell death. Apoptotic, or programmed cell death capability in the p53 network, is thought to be evolutionarily conserved throughout the development of vertebrate species and was probably established after the divergence of vertebrates and non-vertebrates. DNA metabolism and repair capabilities controlled by p53 may have emerged more recently in evolutionary history to create primate-specific response characteristics, the researchers explained.

"The fact that DNA metabolism and repair genes have undergone this kind of evolution in humans may reflect an increased need for coordinated control of molecular repair activities during DNA replication to allow for the maintenance of genomic integrity during complex differentiation, growth and aging," said Bruce Aronow, Ph.D., co-director of Computational Medicine at Cincinnati Children's and a study co-author.

A clue to p53 functional differences may be found in sunlight. Exposure to the ultra-violet rays in sunlight activates the DNA-damage responses of the repair gene Ddb2 in humans, but the same gene does not function in rodents. Some studies have suggested that rodents may have a reduced need for genetic protection from sunlight because they are nocturnal and have a fur shield.

"Although the full implications of these evolutionary points remain far from clear, our work demonstrates that there has been both refinement and evolution of gene networks controlled by p53," Aronow said. "Exciting work is underway by research groups within the National Cancer Institute's Mouse Models of Human Cancer Consortium to develop mice that are genetically engineered to test the combined effects of altering p53 and telomerase, the enzyme that controls the length and stability of repeating DNA sequences in the telomere region. Mouse models will continue to become progressively more powerful tools for studying human cancer and additional information about the p53 network will help us refine our interpretation of pre-clinical research that may lead to improved cancer prevention for at-risk and normal individuals." The present results demonstrate the need for caution in interpreting the observations with mice.

The functional studies in mammalian cells were provided by Daniel Menendez, Ph.D., a research fellow at NIEHS. Alberto Inga, Ph.D., a former NIEHS research fellow, now with his own lab at the National Institute for Cancer Research (Molecular Mutagenesis Unit, Department of Translational Oncology) in Genoa, Italy, provided the initial functional work in yeast that formed the basis for much of the study.

Funding support came in part from the National Cancer Institute's Mouse Models of Human Cancers Consortium, the Italian Association for Cancer Research, the National Institute of Environmental Health Sciences, and the Computational Medicine Center, a State of Ohio Third Frontier Wright Center for Innovation.

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