The modENCODE project takes advantage of many of the same tools and has developed some new ones to apply to the smaller and therefore more tractable genomes of the fruit fly and the roundworm. Unlike the researchers in 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.
To analyze the fruit fly and roundworm genomes, researchers studied many different cell types and developmental stages to produce the catalogs of functional genomic elements. In addition to genes that code for proteins, these functional elements include non-protein-coding genes; regulatory elements that control gene transcription; and DNA sequences that mediate the structure and dynamics of chromosomes.
In the newly published papers, the fruit fly and roundworm researchers report the discovery of hundreds of new protein-coding genes. For instance, in the roundworm genome there is now evidence for thousands of new and refined gene transcripts instructions from genes that produce proteins along with thousands of new non-protein coding RNAs (ncRNAs), which regulate gene expression.
"We now know when these genes are used in the life cycle and increasingly what cells the genes are used in," said Robert H. Waterston, M.D., Ph.D., senior author of the roundworm paper and chair of the Department of Genome Sciences, University of Washington in Seattle. "Putting the pieces together has begun to reveal how genes may work in concert to produce the marvelous biology of the roundworm and fruit fly."
"Identification of thousands of new gene transcripts has significantly increased our knowledge of the protein repertoire used in fruit flies," said Susan Celniker, Ph.D., co-author of the fruit fly paper and head of
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NIH/National Human Genome Research Institute