Kellis and modENCODE Consortium publish major foundational genomic study

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December 31, 2010

EECS associate professor Manolis Kellis, principal investigator in the Computer Science and Artificial Intelligence Laboratory (CSAIL) working with members of the model organism ENCyclopedia Of DNA Elements Consortium (modENCODE) published in Science, Dec. 22, 2010, an integrative study of the Drosophila (fruitfly)--providing a foundation for years of further study into the functional elements shared by both humans and fruit flies. The findings should provide scientists a better understanding of human biology, gene regulation and how the body reacts to disease--information which can be used in medical studies.

Kellis stated for the CSAIL Dec. 22, 2010, news site: “This is everything a computational biologist would wish for for Christmas, but is too shy to ask. This is the first time this amount of data is available on a single organism across such a diverse range of phenotypes,” explained Kellis. “By probing the cell with dozens of different types of experiments, systematically and uniformly across different conditions, modENCODE has provided computational biologists a treasure trove of information, which is a dream come true for large-scale data mining.”

Additionally, the consortium's analysis included the roundworm. Both modENCODE projects were launched in 2007 to complement the work being done by the ENCyclopedia Of DNA Elements Consortium (ENCODE), which is building a comprehensive catalog of elements in the human genome crucial to biological function. In 2007, ENCODE completed a pilot project that developed innovative methods and technologies to find functional elements in about 1 percent of the human genome.

modENCODE takes advantage of many of the same tools, but applies them to the smaller, and therefore more manageable, genomes of the fruit fly and the roundworm. Unlike the human effort, modENCODE researchers can conduct genetic experiments on flies or worms to validate the biological relevance of the functional elements they have identified. By combining and comparing data from worms, flies and humans, researchers can learn far more about the functional elements than if they analyzed the genome of just one species.

To produce the functional analysis of the fly and worm genomes, researchers studied many different cell types and stages of development to produce the preliminary catalogs of functional elements. In addition to genes that code for proteins, these functional parts include non-protein-coding genes; regulatory elements involved in the control of gene transcription; and DNA sequences that mediate the structure and dynamics of chromosomes.

The Science paper titled, "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE" concludes: "Given the extensive conservation of biological molecules and processes between flies and vertebrates, these will not only improve our understanding of fly biology, but can also serve as a template for understanding of human biology and disease."

Read more:

CSAIL News, Dec. 22, 2010, "Learning from the Fruit Fly"

Science, Dec. 22, 2010 Hot Topic: Genomic Analyses of C. elegans and D. melanogaster

Nature, Dec. 22, 2010: "Comprehensive analysis of the chromatin landscape in Drosophila melanogaster"