Muscling in on chromosomal clusters

It is becoming increasing apparent that eukaryotic genomes are organized into regions containing clusters of co-regulated genes. In the August 29 Nature, Roy et al. describe clusters of muscle-expressing genes in the Caenorhabditis elegans genome (Nature 2002, 418:975-979). They developed a method called 'messenger RNA tagging' that uses immunoprecipitation of an epitope-tagged RNA-binding protein to purify mRNA expressed in different tissues; they then used DNA microarrays to analyse the enrichment of co-immunoprecipitated mRNAs. Roy et al. found over 1,000 genes that were consistently enriched in six muscle mRNA-tagging experiments. When they mapped the chromosomal locations of these genes, they found that almost a third of them are positioned within 10kb of another muscle-expressed gene. Many of the muscle genes are found in clusters of 2-5 genes, sometimes interrupted by a non-expressed gene. Additional analysis provided evidence for clustering of genes expressed in sperm or oocytes. Roy et al. speculate that gene clusters may represent regions of active chromatin.