The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in @entity1 culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only    40% of the annotated 622 @entity1 tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the @entity19 liver. Our studies define the @entity19 liver RNAP-III-occupied loci including a conserved @entity1 interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of @entity1 and @entity19 RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In @entity19 liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine @entity69879 (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing @entity1 culture cells and resting @entity19 liver cells, and the particular promoter and terminator strengths of individual genes.

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in XXXX liver.

@entity1 :: ('9606', 'Species') :: ['mammalian', 'human'] @entity69879 :: ('19799(Tax:10090)', 'Gene') :: ['Rn4.5s'] @entity19 :: ('10090', 'Species') :: ['mouse']
@entity19 :: (10090,Species) :: ['mouse']
