Functional genomics

A genomewide functional network for the laboratory mouse. Guan, Y. et al. PLoS Comp. Biol. 4, e1000165 (2008)

The authors have generated a global functional network for the mouse by integrating various genetic and functional genome-wide data sets using a probabilistic model. This community resource (which is freely available at http://mouseNET.princeton.edu) predicts the probability that two proteins are involved in the same biological process. It encompasses linkages between over 20,000 protein-coding genes and can be used to discover protein functions and novel pathway components as well as for exploring the general features of cellular interactomes.

Circadian clocks

A morning-specific phytohormone gene expression program underlying rhythmic plant growth. Michael, T. P. et al. PLoS Biol. 6, e225 (2008)

The rate of plant growth varies during the light–dark cycle and is controlled by external signals and the plant's intrinsic circadian clock. In this study the authors characterize the transcriptome of Arabidopsis thaliana under different growth conditions and propose a model in which the circadian clock controls growth rate by restricting when transcription of growth-promoting hormones can occur. Coordination of transcription with circadian and diurnal rhythms involves a cis-acting element in the promoters of hormone genes.

RNA world

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Grimson, A. et al. Nature 1 Oct 2008 (doi: 10.1038/nature07415)

It has been hypothesized that microRNAs (miRNAs) emerged alongside increased complexity in bilaterian animals. By sequencing organisms from basal metazoan phyla, such as a sponge and a sea anemone, these authors found that both miRNAs and piwi-interacting RNAs have been present since the beginning of metazoan evolution. They report that miRNA evolution has been highly dynamic in animal lineages, producing diverse precursor-miRNA lengths and miRNA sequences between phyla, and loss of all miRNAs in the placozoan Trichoplax adhaerens.

Genomics

Retention of induced mutations in a Drosophila reverse-genetic resource. Cooper, J. L. et al. Genetics 180, 661–667 (2008)

This study provided the first large-scale quantitative assessment of a genetic repository of breeding Drosophila melanogaster lines (Fly-TILL). The stability of ethyl methanesulphonate (EMS)-induced mutations was evaluated: although balancer chromosomes were used to maintain the mutagenized chromosomes in a heterozygous state, local recombination with the balancer might have resulted in loss of mutations. Analysis of nearly 2,000 EMS-induced point mutations (over 100 generations) indicated that although selection and differential retention had occurred, the collection was sufficiently stable to be used as a long-term genetic resource.