A news story in Nature this week reports on the FANTOM consortium, which used high-throughput sequencing to create a timeline of mRNA produced by human leukemia cells in response to the presence of phorbol myristate acetate. They used RNAi across 52 transcription factors to verify the identity of key transcription regulators, their time-dependent activities, and target genes. "Although similar models have been constructed for yeast, the FANTOM project is the most in-depth study to date of human gene regulatory networks," says the news story.
While Nature has launched a new journal, Nature Chemistry, it dedicates this issue to former editor John Maddox, who passed away on April 12. Maddox was editor of Nature from 1966-1973 and 1980-1995, and "transformed the journal from a collegially amateurish publication into one that was challenging and professional in its assessment of science and in its journalistic reportage," says the obituary. A special section pays tribute.
Scientists used a genome-wide RNAi screen to examine the Notch signaling pathway during external sensory organ development in Drosophila, the first such screen used to look at a tissue-specific complex developmental process. They assigned putative loss-of-function phenotypes to 21.2 percent of the protein-coding Drosophila genes and identified six new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signaling pathway, they say in the abstract. They followed it up with integrative data analysis, building a genome-wide interaction network for Notch signaling and asymmetric cell division.
Duke scientists also used a genome-wide RNAi screen to find host factors required for the infection and spread of the Dengue fever virus. The screen identified 116 candidate dengue virus host factors (DVHFs). The dipteran DVHFs had 82 human homologues, they found, and using a targeted screen they showed that 42 of these are human DVHFs. "This indicates notable conservation of required factors between dipteran and human hosts," they say in the abstract, which could help find new ways to fight infection.