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E-GEOD-38382 - RNA polymerase II collision interrupts convergent transcription (ChIP-seq)

Status
Released on 30 November 2012, last updated on 11 January 2013
Organism
Saccharomyces cerevisiae
Samples (8)
Protocols (4)
Description
Anti-sense non-coding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical and genetic approaches in yeast to show that polymerases transcribing opposite DNA strands cannot bypass each other. RNAPII stops, but does not dissociate upon head-to-head collision in vitro, suggesting that opposing polymerases represent insurmountable obstacles for each other. Head-to-head collision in vivo results in RNAPII stopping as well, and removal of collided RNAPII from the DNA template can be achieved via ubiquitylation-directed proteolysis. Indeed, in cells lacking efficient RNAPII poly-ubiquitylation, the half-life of collided polymerases increases, so that these can be detected between convergent genes by ChIP-Seq. These results provide new insight into fundamental mechanisms of gene traffic control, and point to an unexplored effect of anti-sense transcription on gene regulation via polymerase collision. ChIP-Seq of RNA polymerase II was performed with WT and Elongain C deletion mutant (elc1∆) cells. 4H8 antibody against the Rpb1 C-terminal domain was used for RNA polymerase II immunoprecipitation, whilst mouse IgG antibody was used for control immunoprecipitations. Two biological replicates were performed for both WT and elc1∆.
Experiment type
ChIP-seq 
Contacts
Wu Wei <wuwei@embl.de>, David J Hobson, Jesper Q Svejstrup, Lars Steinmetz
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-38382.idf.txt
Sample and data relationshipE-GEOD-38382.sdrf.txt
Processed data (2)E-GEOD-38382.processed.1.zip, E-GEOD-38382.processed.2.zip
Links