Mus musculus strain:C57/BL6 Transcriptome or Gene expression. Mus musculus strain:C57/BL6

The RNA polymerase III transcriptome has been studied in human culture cells by genome-wide chromatin immunoprecipitation experiments followed by deep sequencing (ChIP-Seq). These studies have in particular shown that only about 40% of the annotated 622 human tRNA genes and pseudogenes are transcribed, and that these genes are often in regions of open chromatin rich in active pol II transcription units. We have used ChIP-Seq to characterize the pol III transcriptome in a differentiated tissue, the mouse liver. Principal Findings: These studies define the mouse liver pol III transcriptome and point to a conserved pol III-occupied MIR as a potential regulator of a pol III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse pol III genes, and that the expression levels of these genes are significantly linked. They reveal correlations with various genomic features that together describe the pol III occupancy scores over some 50% of tRNA genes. Conclusions/Significance: In mouse liver, the pol III transcriptome consists of fifty 5S genes, fourteen known non-tRNA genes, nine 4.5S genes, and some twenty nine SINEs. Of the 433 annotated tRNA genes, 50% are occupied by pol III. Transfer RNA gene expression levels reflect both an underlying genomic organization that is conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.