In Science this week, members of the model organism Encyclopedia of DNA Elements — or modENCODE — Consortium present their findings from the more than 700 data sets they've generated by "mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines" in Drosophila. The modENCODE researchers say that their study provides a foundation upon which further experimental and computational analyses can be conducted using this model organism and also serves as a "model for systematic data integration toward comprehensive genomic and functional annotation."
Members of modENCODE also report their "integrative analysis of the Caenorhabditis elegans genome" in this week's Science. The team generated large-scale data sets for the nematode, which include "transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization." Using this information, the team was able to create "more complete and accurate gene models," which include, among other things, alternative splice forms and candidate non-coding RNAs. In addition, the modENCODE group "constructed hierarchical networks of transcription factor–binding and microRNA interactions," with which they "discovered chromosomal locations bound by an unusually large number of transcription factors," the authors write.
Researchers at the Institute for Research in Biomedicine in Barcelona show that the "ectopic expression of germline genes drives malignant brain tumor growth in Drosophila." More specifically, mutations in the fruit fly gene lethal (3) malignant brain tumor — which "cause malignant growth in the larval brain," the authors note — show a soma-to-germline transformation when genes that are "normally required for germline 'stemness,' fitness, or longevity" are ectopically expressed. Human somatic tumors express orthologs of some of these genes, the authors show, adding that the " inactivation of any of the germline genes nanos, vasa, piwi, or aubergine suppressed l(3)mbt malignant growth," in their investigations.
Wentao Li and Roger Chetelat at the University of California, Davis, have found that "Solanum, a pollen-expressed Cullin1 gene with high similarity to Petunia [self-incompatibilty] factors interacts genetically with a gene at or near the S locus to control [unilateral interspecific incompatibility]" in Solanaceae plants. In this week's Science, Li and Chetelat also show that red- and orange-fruited self-compatible species show this loss-of-function mutation, while green-fruited species have a functional allele.