A Genome-Wide Map of Active Gene Promoters

Abstract

June 29, 2005Study Marks First Step in Decoding Gene Regulatory Logic

Investigators from the University California, San Diego (UCSD) Branch of the Ludwig Institute for Cancer Research (LICR) and NimbleGen Systems have developed an efficient method to identify thousands of regulatory sequences in the human genome, according to a study published online on June 29, 2005 in Nature.

Genes are defined by their ability to generate a functional product. Thus the 'promoter' - a DNA sequence that controls when and where a gene product is generated - is the critical element that distinguishes a gene from 'junk DNA.' Using a set of NimbleGen's DNA microarrays that represent the entire human genome, the team was able to track critical proteins binding to each gene's promoter to identify 10,567 active promoters, 5,449 of which were previously unknown.

LICR's Dr. Bing Ren, the senior author of the study and a faculty member at the UCSD School of Medicine, says that although scientists have found most of the protein-coding genes in the human genome, their control sequences have been elusive until now. "Promoters are a type of genetic switch that turn gene expression on or off. If we know where the promoters are, we can study how the genetic switches work in a cell, and investigate their connection to human diseases," said Dr. Ren, who is also a member of the Rebecca and John Moores UCSD Cancer Center. He and his colleagues have made the data freely available on online public databases.

Dr. Robert Strausberg, Vice-President of Human Genomic Medicine at the J. Craig Venter Institute, says that this understanding is vital for determining the genetic causes of, and possible genomic solutions for, diseases such as cancer. "Medicine is increasingly turning towards the idea of using genetic markers for diagnosis and prognosis, or determining personalized therapies, so-called pharmacogenetics, but we don't know how these genes are regulated or even related to each other. The identification of such a large number of promoters means that we can begin to answer these sorts of questions."