SCIENCE

The promise of modENCODE

Of the modENCODE project, Celniker says, “The goal is not only to map every base in the genome but to discover the function of every base.” Adds Karpen, “Discovering function starts with mapping all the components that affect it.”

The results of the modENCODE research go into a central, publicly accessible database. Karpen says, “This information is available for any scientist to use in designing and conducting his or her own experiments. They can use our data to interrogate their favorite genes or the entire genome. It’s from their creativity and ingenuity that progress in understanding the flow of information from sequence to cell and organismal functions will be made.”

From the genomes of model organisms like the fruit fly and the roundworm, says Celniker, “We would like to crack the genomic code and discover the rules required to read a genome – any genome. Knowing which signals control gene expression in the fruit fly and the roundworm, including how chromatin affects gene expression, will be applicable to understanding how to read the human genome."

" Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE,” by the Drosophila modENCODE Consortium, appears in the 24 December 2010 issue of Science and is now online. The Consortium’s transcriptome group, led by Berkeley Lab’s Susan Celniker, includes research teams led by Brenton Graveley of the University of Connecticut Health Center, Peter Cherbas of Indiana University Bloomington, Tom Gingeras of Cold Spring Harbor Laboratory, Norbert Perrimon of Harvard Medical School, Michael Brent of Washington University in Saint Louis, and Steven Brenner of the University of California at Berkeley. The chromatin group, led by Gary Karpen of Berkeley Lab and UC Berkeley, includes teams led by Sarah Elgin of Washington University in Saint Louis, Mitzi Kuroda of Harvard Medical School, Peter Park of Harvard Medical School, and Vince Pirrotta of Rutgers University.

“The developmental transcriptome of Drosophila melanogaster,” by members of the transcriptome group, and “Comprehensive analysis of the chromatin landscape in Drosophila melanogaster,” by members of the chromatin group, now appears in advance online publication of Nature.

Forthcoming papers on promoter architecture, by Celniker and first author Roger Hoskins of her team at Berkeley Lab; on transcriptional profiling of Drosophila cell lines, by Lucy and Peter Cherbas of the Celniker group; and on chromatin organization of heterochromatin by the Karpen group, including co-first author Aki Minoda of Berkeley Lab, will appear in a forthcoming issue of Genome Research devoted to modENCODE studies.