ENCODE Unveiling the Next Big Leap in Understanding Human Genome

After five years of concerted effort by more than 440 researchers in 32 labs around the world, working collaboratively on the ENCODE Project, the first holistic view of how the human genome actually does its job has emerged. The international, collaborative effort mapped more than 4 million regulatory regions where proteins specifically interact with DNA and attributed a biochemical function to more than 80 percent of the human genome.

Greg CrawfordAssistant professor, pediatrics, Duke Institute for Genome Sciences & Policygreg.crawford@duke.eduhttp://genome.duke.edu/directory/faculty/crawford/ As a member of the ENCODE Consortium, Crawford's research involved the identification of gene regulatory elements across the genome to help in understanding how DNA structure dictates cell function and fate. Quote:"We've had the linear DNA sequence, but we didn't fully know what this linear DNA sequence was telling us. ENCODE has made it possible to really understand all of the really important parts of the genome -- where they are located, what proteins bind there, and how that relates to global gene expression. It is shedding light on the key pieces of the genome that are critical for turning genes on and off across the genome. "We've used a general method to identify all of the gene switches across 100 cell types. Only about 3 percent of the genome is made up of genes. In any given cell type, another 1 or 2 percent of the genome is made up of regulatory switches. By looking at 100 cell types, we find that it's a lot more than that when you add it all together. We see now that some 15 to 20 percent is functional across cell types and we don't know how high that number will go as scientists look at more and more cell types. "This is just the beginning. It's the tip of the iceberg. Now we know which regions are important and we have a hint about what they are doing, but we need to study these regions in detail to fully understand it." Tim ReddyAssistant professor, Biostatistics & Bioinformatics, Duke Institute for Genome Sciences & Policytim.reddy@duke.eduhttp://genome.duke.edu/directory/faculty/reddy/  Reddy is interested in studying mechanisms of tissue­specific gene control. He contributed to the ENCODE project as a lead analyst. Quote:"When the Human Genome Project was finished more than 10 years ago, we still didn't know what the vast majority of it meant. There is still a lot we don't know, but this is a step in the direction to actually understanding it. We knew back then where many of the genes were, but those genes only account for about 3 percent of the genome. ENCODE tells us where the controls are; it starts to fill in the 97 percent gap we had in our understanding.  "This is important for disease studies because much of the variation that's been connected to diseases has been found in regions involved in how genes are regulated as opposed to their structure. Now that we know where those control elements are, we can start to understand how diseases are the result of changes in regulation. It leads us to new mechanisms.  "This is one of the biggest steps forward since the human genome was sequenced, and I'm really excited to see what happens next. The steps keep getting bigger, and I'm sure the next phase will feel like a leap."