Farnham, Peggy J. Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California.
- What has been learned from ENCODE?
- About 60% of the genome is transcribed into some form of RNA
- About 95% of the genome lies within 8 kilobases of a protein--DNA interaction
- The genome has a highly complex interactive structure
- Insights into human health
- Further exploration
- Links to Primary Literature
- Additional Readings
Many human diseases are caused by changes in the abundance or activity of proteins, and proteins are encoded by segments of DNA called genes. Therefore, a logical assumption is that identifying all the human genes could help in understanding human disease. The Human Genome Project was launched in 1990 with this specific goal in mind. This led to a push for sequencing the entire genome, which began in 1996, with a draft version of the human genome being published in 2001. One of the first big surprises that came from this era of human genomics had to do with the number of genes that was found. Based on the fact that genomic sequencing of a worm (which has only 959 cells and 1 × 108 nucleotides of DNA) had identified approximately 20,000 genes, it was assumed that humans would have approximately 150,000 genes (after all, a human is much more complicated than a worm). However, after the human genome was sequenced and “read” by computational programs that compared the results to known proteins and RNAs (the intermediary nucleic acids from which proteins are encoded), the results suggested that humans might have at most 30,000 genes; refinement of the analyses has since reduced this number to 20,000. In other words, a human has the same number of genes as a worm. In fact, only 5% of the 3 × 109 nucleotides in the human genome is covered by exons (DNA segments that encode proteins). This realization led to an intriguing question: If 95% of the genome is not involved in coding for proteins, then what does it do? A large international consortium called ENCODE (Encyclopedia of DNA Elements), funded by the National Human Genome Research Institute, began to address this question in 2004, and a pilot project was undertaken to study 1% of the human genome. However, ENCODE quickly advanced to studying the entire genome by 2007 because of technological improvements. The assays chosen by the ENCODE consortium focused on identifying regions of the genome that are “in use”—for example, regions that are transcribed into RNA or regions that control whether a gene is turned on or off. Since 2007, 442 scientists from 32 different institutes have studied 147 cell types and collected more than 1640 data sets; these efforts from the ENCODE consortium have shed light on several important questions in human biology.
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