Transcriptional profile of rat extraocular muscle by serial analysis of gene expression.

PURPOSE Although extraocular muscle (EOM) is skeletal muscle, aspects of its biology are unlike other striated muscle. In this study, the broad molecular genetics profile underlying the novel EOM phenotype was examined. METHODS Serial analysis of gene expression (SAGE) was used to quantify adult rat EOM gene transcripts. SAGE isolates and sequences 10-bp tags from defined locations in mRNA-derived cDNA. Tag sequence-location was used to extract transcript identity from a curated SAGE database, and detection frequencies reflected abundance of corresponding mRNAs. RESULTS The 54,764 expressed sequence tags generated and sequenced from EOM included 17,602 unique tags. Of the unique tags, 7.8% were detected at high to intermediate levels (>or=5 copies), 19.3% at lower levels (2-4 copies), and 72.9% as single copies; 40% of the tags matched known expressed sequence tags (ESTs), most of which (85.7%) represented a unique EST. Tags without matches in the SAGE database and those expressed as single copies only were not considered further. SAGE tags expressed at more than 0.1% of total transcripts reflected several aspects of muscle biology, including sarcomeric structure, energy metabolism, and ribosomal protein expression. Genes highly expressed in EOM were compared with other existing muscle expression databases to identify conserved and novel patterns in EOM. CONCLUSIONS The data provide a normative gene expression database and a novel molecular signature that will facilitate study of EOM development and function and of the mechanisms behind its preferential targeting or sparing in neuromuscular disease.