modENCODE

The modENCODE project (model organism encyclopedia of DNA elements) is a collaborative effort to identify all sequence-based functional elements of Drosophila and C. elegans. The project has now produced almost a thousand data sets with information about transcription, epigenetics, replication and gene regulation across different developmental stages and multiple cell lines.

Just before the holidays, the modENCODE teams published several analyses of these data sets in a number of papers across four journals. Because the data were collected across multiple developmental stages, they give information that cannot be gathered from looking at just one point in development.

In a CSHL podcast, modENCODE team member Thomas Gingeras describes work from his group that was published in Science. They used the modENCODE data to confirm that 90% of all 17 thousand predicted protein coding regions in Drosophila indeed correspond to RNA expression. At any given point along the developmental timeline, this percentage would of course be a lot smaller, as genes switch on and off. In addition, they found almost two thousand previously unannotated genes.

Another result relevant to developmental biologists is covered in one of the Nature papers: An analysis of different chromatin states in Drosophila revealed a more complex pattern of Polycomb target regulation than was previously suspected.

Worm researchers also have a lot of new information to work with. For example, a Science paper describes the mapping of transcription factor binding sites in C. elegans and reports that some regions of the worm genome – which they called HOT regions – were bound by more than 15 transcription factors!

So what’s next for the modENCODE project? There is still a year of funding left, and much of that time will be spent adding more annotations for newly found functional regions, as well as integrating different types of data for a more complete picture.

Of course, the worm and fly are not the only organisms to be mapped. Let’s not forget ourselves! The (human) ENCODE project, which in fact precedes modENCODE, hopes to publish a full genome analysis next year.

References:

The modENCODE Consortium, ., Roy, S., Ernst, J., Kharchenko, P., Kheradpour, P., Negre, N., Eaton, M., Landolin, J., Bristow, C., Ma, L., Lin, M., Washietl, S., Arshinoff, B., Ay, F., Meyer, P., Robine, N., Washington, N., Di Stefano, et al. (2010). Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE Science, 330 (6012), 1787-1797 DOI: 10.1126/science.1198374

Kharchenko, P., Alekseyenko, A., Schwartz, Y., Minoda, A., Riddle, N., Ernst, J., Sabo, P., Larschan, E., Gorchakov, A., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, M., Luquette, L., Xi, R., Jung, Y., Park, R., Bishop, E., Canfield, T., Sandstrom, R., Thurman, R., MacAlpine, D., Stamatoyannopoulos, J., Kellis, M., Elgin, S., Kuroda, M., Pirrotta, V., Karpen, G., & Park, P. (2010). Comprehensive analysis of the chromatin landscape in Drosophila melanogaster Nature DOI: 10.1038/nature09725

Gerstein, M., Lu, Z., Van Nostrand, E., Cheng, C., Arshinoff, B., Liu, T., Yip, K., Robilotto, R., Rechtsteiner, A., Ikegami, K., Alves, P., Chateigner, A., Perry, M., Morris, M., Auerbach, R., Feng, X., Leng, J., Vielle, A., Niu, W., Rhrissorrakrai, et al. (2010). Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project Science, 330 (6012), 1775-1787 DOI: 10.1126/science.1196914

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