Functional Genomics

Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Hirai, M. Y. et al. Proc. Natl Acad. Sci. USA 15 June 2004 (doi:10.1073/pnas0403218101)

Few studies have managed to integrate global analyses of gene expression and metabolism. Masami Hirai and colleagues do just that for Arabidopsis thaliana, specifically focussing on the effects of sulphur deficiency. Their multidimensional analyses of DNA macroarray and mass-spectrometry data allowed them to identify metabolic pathways that respond to nutrient deficiencies. The expression of genes in the glucosinolate metabolic pathway is particularly tightly coordinated with this pathway's metabolites.

Mouse Genetics

Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. Yalcin, B. et al. Proc. Natl Acad. Sci. USA 29 June 2004 (doi:10.1073/pnas0401189101)

Variation between the genomes of inbred mouse strains was thought to be structured into high- and low-frequency segments that might be useful for quantitative trait locus (QTL) mapping. Richard Mott and colleagues show that, for one region at least, this picture is inaccurate: while the distribution of variation between mouse strains is not random, the definition of haplotype blocks is problematic. Complete sequences might be needed to map QTLs from the distribution of SNP variants among strains.

Community Resource

The BDGP Gene Disruption Project: single transposon insertions associated with 40% of Drosophila genes. Bellen, H. J. et al. Genetics 167, 761–781 (2004)

The Berkeley Drosophila Genome Project (BDGP) aims to disrupt each fly gene with a single P-transposon insertion. This article reports the expansion of the collection from 1,045 to 7,140 lines — targeting ∼5,362 (or 39%) of annotated D. melanogaster genes — which are freely available to the community. This is a valuable resource for fly geneticists that also provides insight into how transposons interact with the eukaryotic genome.

Community Resource

Mutagenic insertion and chromosome engineering resource (MICER). Adams, D. J. et al. Nature Genet. 4 July 2004 (doi:10.1038/ng1388)

The manipulation of mouse embryonic stem cells remains the preferred way to assess the function of mouse genes. To overcome the limitation caused by gene targeting — which requires unique vectors to be designed for each target allele — the authors have created a public resource (MICER) that consists of 93,960 insertional targeting vectors. A total of 5,925 of these, which were indexed from 2 existing vector libraries, can be readily used to inactivate specific genes or to engineer larger genomic alterations.