Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA polymerase II collision interrupts convergent transcription (RNA-seq)

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE38383 | GEO | 2012/11/30

SECONDARY ACCESSION(S): PRJNA167772

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA polymerase II collision interrupts convergent transcription (RNA-seq)

Project 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. Total RNA was extracted from WT or Elongin C deletion mutant (elc1M-bM-^HM-^F) cells and strand-specific RNA-Seq was performed. Three biological replicates were performed for WT and elc1M-bM-^HM-^F.

2012-11-30 | E-GEOD-38383 | biostudies-arrayexpress

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

Project 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 (elc1M-bM-^HM-^F) 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 elc1M-bM-^HM-^F.

2012-11-30 | E-GEOD-38382 | biostudies-arrayexpress

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

2012-11-30 | GSE38382 | GEO

Genome-wide survey of ribosome collision [anisomycin]

Project description:In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. Here we surveyed the position of ribosome collisions, caused by ribosome pausing, at a genome-wide level using the modified ribosome profiling in human and zebrafish. The collided ribosomes, i.e. disome, emerge at various sites; the proline-proline-lysine motif, stop codons, and 3′ UTR. The number of ribosomes in a collision is not limited to two, rather four to five, forming a queue of ribosomes. Especially, XBP1, a key modulator of unfolded protein response, shows striking queues of collided ribosomes thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and the consequences of ribosome slowdowns by dissecting the specific architecture of ribosomes.

2020-05-05 | GSE140639 | GEO

Genome-wide survey of ribosome collision [eif5A siRNA]

2020-05-05 | GSE145722 | GEO

Genome-wide survey of ribosome collision [monosome/disome]

2020-05-05 | GSE133393 | GEO

Genome-wide survey of ribosome collision

Project description:Genome-wide survey of ribosome collision

| PRJNA607993 | ENA

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag]

Project description:Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.

2022-09-16 | GSE210181 | GEO

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-Seq]

2022-09-16 | GSE211862 | GEO

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [4tU-seq]

Project description:Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. However, the genome-wide requirement for Spt5 in transcription has not been extensively studied. To address this issue, we have comprehensively analyzed the consequences of Spt5 depletion on transcription by RNAPII in Schizosaccharomyces pombe using four genome-wide approaches: ChIP-seq, NET-seq, 4tU-seq, and RNA-seq. Our results demonstrate that, in the absence of Spt5, RNAPII accumulates at a high level over the first ~500 bp of transcription units, suggesting that Spt5 is globally required to elongate past a barrier to transcription. This possibility is strongly supported by results showing that Spt5 is required for a normal level of RNA synthesis. In addition to these effects on sense-strand transcription, Spt5 depletion results in widespread convergent antisense transcription that initiates at approximately the same position as the sense-strand barrier. While the role of these antisense transcripts is unknown, the two that were tested control the distribution of RNAPII. Our results also show that Spt5 represses divergent antisense transcription, explaining why it has not been previously observed in S. pombe. Taken together, our results reveal a global and critical role for Spt5 in multiple classes of transcription by RNAPII.

2017-03-30 | GSE85181 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data