title: A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver.
abstract: The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human 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 mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian 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 human and mouse 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 mouse 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 Rn4.5s (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 human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.
authors.affiliation: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Donatella
authors.initials: D
authors.lastname: Canella
authors.forename: David
authors.initials: D
authors.lastname: Bernasconi
authors.forename: Federica
authors.initials: F
authors.lastname: Gilardi
authors.forename: Gwendal
authors.initials: G
authors.lastname: LeMartelot
authors.forename: Eugenia
authors.initials: E
authors.lastname: Migliavacca
authors.forename: Viviane
authors.initials: V
authors.lastname: Praz
authors.forename: Pascal
authors.initials: P
authors.lastname: Cousin
authors.forename: Mauro
authors.initials: M
authors.lastname: Delorenzi
authors.forename: Nouria
authors.initials: N
authors.lastname: Hernandez
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006801:Humans; D008099:Liver / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012320:RNA Polymerase III / Q000235:genetics* / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D012343:RNA, Transfer; D012320:RNA Polymerase III