The Encyclopedia of DNA Elements (ENCODE) consortium published a set of papers in Nature and Genome Research that sum the work of more than four years of effort dedicated to understanding the functional elements of the human genome-a step toward the goal of using such information to diagnose, treat and prevent disease.
NimbleGen Systems, Inc. played a primary role in this international discovery effort, both as the chosen chromatin immunoprecipitation microarray (ChIP-chip) platform for a majority of investigators who participated in this study and as the recipient of $2.5 million in ENCODE research grants. At least 15 papers have been published to date by ENCODE participants using the NimbleGen platform.
“With the innovative microarray technologies that NimbleGen provides, we have been able to identify the transcription factor binding sites and chromatin modifications along the human genome in multiple cell types,” stated Dr. Bing Ren, assistant professor at the University of California, San Diego School of Medicine and Ludwig Institute for Cancer Research (LICR), and participant in the ENCODE consortium.
“The high quality data from such experiments have allowed us to annotate promoters, enhancers, insulators and other transcriptional regulatory elements in the human genome and examine the mechanisms that drive cell type-specific gene expression programs in human cells. We anticipate that this information will provide a valuable resource for study of human development, disease process and evolution.”
Begun in September 2003 by the National Human Genome Research Institute (NHGRI), the ENCODE project picks up the search for understanding the human genome where the Human Genome Project left off.
Composed of scientists from 35 groups within 80 organizations in government, industry, and academia across the world, ENCODE is dedicated to producing a catalog of elements crucial to biological function in the roughly 98 percent of the human genome that does not code for proteins. Approximately 1% of the human genome, or 30 million DNA base pairs, was selected for in-depth investigation; the targets were strategically selected to provide a representative cross section of the entire human genome.
The results have led researchers to rethink some long-held views about what genes are and what they do, as well as how the genome’s functional elements have evolved.
The ENCODE consortium’s major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called “junk” DNA that is not biologically active. The new data indicate the genome contains very little unused sequences and is a complex, interwoven network.
NimbleGen’s ChIP-chip technology was the primary ChIP-chip platform for ENCODE research on regulation of gene expression. “We chose NimbleGen because of its ability to produce arrays with long oligonucleotide probes, which allows for higher sensitivity and specificity. The capacity for flexible design and high probe density also made the NimbleGen platform a good choice,” stated Dr. Jason Lieb, assistant professor in the Department of Biology at University of North Carolina.
Lieb and researchers at UNC developed a method for mapping regions of a wide range of genomes that are depleted of nucleosomes, a hallmark of gene activity. Using a method termed FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements), the group was able to distinguish active and inactive regions of the genome and compare these patterns between different cell types.
The method utilizes NimbleGen high-density DNA arrays to map regions of chromatin activity at high resolution, genome wide. Distinguishing patterns of chromatin activity provides insight on cellular regulatory processes in both normal and diseased cells.
“Our experiments proved that FAIRE, a new technology developed under the ENCODE project, is a simple and effective method for high-throughput mapping of open chromatin throughout the human genome,” said Lieb. “The high quality of the NimbleGen data allowed us to create the open chromatin maps quickly and at high confidence with relatively few experiments.”
Another ENCODE grant recipient, Peggy Farnham and researchers at the University of California, Davis Genome Center, used NimbleGen ChIP-chip technology to analyze how human cells regulate gene expression by identifying protein binding sites in the genome at high resolution.
“We chose to use NimbleGen arrays for our ENCODE research due to the high sensitivity and reproducibility of the ChIP-chip data,” Farnham stated. “Also, the high signal-to-noise ratio obtained using NimbleGen arrays enabled us to easily compare binding patterns of different transcription factors and allowed us to demonstrate a striking correspondence between binding of E2F family members and RNA polymerase II.”
As the ENCODE project moves into the production phase, NimbleGen’s ChIP-chip technology will be applied to analysing regulation of gene expression in the remaining 99% of the human genome. According to the ENCODE consortium, one of the goals of this project is to establish a reference base against which scientists will subsequently compare variation in regulation of gene expression involving thousands of different factors, in hundreds of target tissues, under numerous conditions.