In Genome Biology this week, Lawrence Berkeley National Lab's Michael Eisen was lead author on a paper that identified a total of 21 transcription factors in the fruit fly that regulate embryo patterning and can bind to overlapping sets of thousands of genomic regions. The high overlap is interesting, the authors say, because the proteins belong to 11 binding domain families, program distinct fates, and can interact with DNA through different cis-regulatory modules. "We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount of bound factor, rather than the identity of bound factors," they write in the abstract.
In research also done in Drosophila, scientists studied the genetics of aggression, specifically the variation in aggressive behavior. A "genome wide association screen for quantitative trait transcripts and single feature polymorphisms affecting aggression" in 40 lines of fruit fly turned up 266 candidate genes associated with aggression, they say. Mutating 12 of these showed that nine affected behavior. They then used this data to create a transcriptional network associated with natural variation in aggressive behavior.
In a methods article, scientists led by researchers at the University of Basel and Swiss Institute of Bioinformatics looked at ways to analyze deep sequencing data from gene expression studies. Using their methods on 122 CAGE samples, they were able to build genome-wide 'promoteromes' in human and mouse comprised of transcription start sites, transcription start clusters, and transcription start regions. In another paper, Finnish scientist led by Laura Elo at the University of Turku developed a new method to statistically analyze alternative splicing data coming off Affymetrix exon arrays. Their method, they say, "shows superior reproducibility and accuracy in distinguishing true biological findings from background noise."
Finally, Chinese scientists used Solexa sequencing to discover microRNAs in the amphioxus species Branchiostoma belcher. They found 113 amphioxus miRNA genes, 55 of which were conserved across species and encoded 45 mature miRNAs, and 58 that were specific to amphioxus and encoded 53 mature miRNAs.