NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE33421 Query DataSets for GSE33421
Status Public on Jan 19, 2012
Title A Multiplicity of Factors Contributes to Selective RNA polymerase III occupancy of a Subset of RNA polymerase III Genes in Mouse Liver
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The genomic loci occupied by RNA polymerase (pol) III have been characterized 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 occupied by pol III, and that these genes are often in regions of open chromatin rich in active pol II transcription units. Here we have used ChIP-Seq to characterize pol III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver pol III-occupied loci and point to a conserved pol III-occupied mammalian interspersed repeat (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 establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence can strongly affect pol III occupancy of tRNA genes. They reveal correlations with various genomic features that together describe the pol III occupancy scores over some 50% of tRNA genes. In mouse liver, pol III-occupied loci represented in the NCBI37/mm9 genome assembly comprise fifty 5S genes, fourteen known non-tRNA genes, nine 4.5S genes, and some twenty nine SINEs. In addition, out of the 433 annotated tRNA genes, half 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.
 
Overall design 12 samples examinded, 4 on pol III, 2 on pol II, 2 on H3K4me3, 2 on H3k36me3, 2 input samples.
 
Contributor(s) Canella D, Bernasconi D, Hernandez N, Delorenzi M
Citation(s) 22287103
Submission date Nov 02, 2011
Last update date May 15, 2019
Contact name David Bernasconi
E-mail(s) nouria.hernandez@unil.ch, donatella.canella@unil.ch, david.bernasconi@unil.ch
Organization name University of Lausanne
Department CIG
Lab Nouria Hernandez
Street address Quartier Sorge, Bat. GĂ©nopode
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (12)
GSM826717 RPC1_Rep1
GSM826718 RPC1_Rep2
GSM826719 RPC4_Rep1
Relations
SRA SRP009177
BioProject PRJNA148919

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE33421_RAW.tar 3.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap