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

Details

Ressource 1Download: 666.pdf (2112.12 [Ko])
State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_AFFF7604F2F3
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver.
Journal
Genome Research
Author(s)
Canella D., Bernasconi D., Gilardi F., LeMartelot G., Migliavacca E., Praz V., Cousin P., Delorenzi M., Hernandez N.
Working group(s)
CycliX Consortium
Contributor(s)
Hernandez N., Delorenzi M., Deplancke B., Desvergne B., Guex N., Herr W., Naef F., Rougemont J., Schibler U., Deplancke B., Guex N., Herr W., Guex N., Andersin T., Cousin P., Gilardi F., Gos P., Le Martelot G., Lammers F., Canella D., Gilardi F., Raghav S., Fabbretti R., Fortier A., Long L., Vlegel V., Xenarios I., Migliavacca E., Praz V., Guex N., Naef F., Rougemont J., David F., Jarosz Y., Kuznetsov D., Liechti R., Martin O., Ross F., Sinclair L., Cajan J., Krier I., Leleu M., Migliavacca E., Molina N., Naldi A., Rey G., Symul L., Guex N., Naef F., Rougemont J., Bernasconi D., Delorenzi M., Andersin T., Canella D., Gilardi F., Le Martelot G., Lammers F., Raghav S.
ISSN
1549-5469 (Electronic)
ISSN-L
1088-9051
Publication state
Published
Issued date
2012
Peer-reviewed
Oui
Volume
22
Number
4
Pages
666-680
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
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.
Keywords
Animals, Chromatin Immunoprecipitation/methods, Gene Expression Profiling, Genomics/methods, Humans, Liver/metabolism, Male, Mice, Mice, Inbred C57BL, Models, Genetic, Oligonucleotide Array Sequence Analysis, RNA Polymerase III/genetics, RNA Polymerase III/metabolism, RNA, Transfer/genetics, RNA, Transfer/metabolism, Sequence Analysis, DNA/methods
Pubmed
Web of science
Create date
14/02/2012 16:07
Last modification date
18/02/2020 7:20
Usage data