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Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo

Overview of attention for article published in Genome Biology, May 2015
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  • Above-average Attention Score compared to outputs of the same age (52nd percentile)

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Title
Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo
Published in
Genome Biology, May 2015
DOI 10.1186/s13059-015-0666-5
Pubmed ID
Authors

Masahiko Imashimizu, Hiroki Takahashi, Taku Oshima, Carl McIntosh, Mikhail Bubunenko, Donald L. Court, Mikhail Kashlev

Abstract

Transcription elongation is frequently interrupted by pausing signals in DNA, with downstream effects on gene expression. Transcription errors also induce prolonged pausing, which can lead to a destabilized genome by interfering with DNA replication. Mechanisms of pausing associated with translocation blocks and misincorporation have been characterized in vitro, but not in vivo. We investigate the pausing pattern of RNA polymerase (RNAP) in E. coli by a novel approach, combining native elongating transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq). We reveal that the G-dC base pair at the 5' end of the RNA-DNA hybrid interferes with RNAP translocation. The distance between the 5' G-dC base pair and the 3' end of RNA fluctuates over a three-nucleotide width. Thus, the G-dC base pair can induce pausing in post-translocated, pre-translocated, and backtracked states of RNAP. Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elongation and induces G-to-A errors, which leads to backtracking of RNAP. Gre factors efficiently proofread the errors and rescue the backtracked complexes. We also find that pausing events are enriched in the 5' untranslated region and antisense transcription of mRNA genes and are reduced in rRNA genes. In E. coli, robust transcriptional pausing involves RNAP interaction with G-dC at the upstream end of the RNA-DNA hybrid, which interferes with translocation. CpG DNA sequences induce transcriptional pausing and G-to-A errors.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 93 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 1%
United Kingdom 1 1%
Finland 1 1%
Spain 1 1%
Unknown 89 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 28 30%
Researcher 10 11%
Student > Master 10 11%
Student > Bachelor 7 8%
Student > Postgraduate 7 8%
Other 13 14%
Unknown 18 19%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 34 37%
Agricultural and Biological Sciences 27 29%
Computer Science 3 3%
Chemistry 3 3%
Engineering 2 2%
Other 4 4%
Unknown 20 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 20 June 2015.
All research outputs
#14,784,344
of 25,374,917 outputs
Outputs from Genome Biology
#3,888
of 4,467 outputs
Outputs of similar age
#132,576
of 279,384 outputs
Outputs of similar age from Genome Biology
#68
of 72 outputs
Altmetric has tracked 25,374,917 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 4,467 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one is in the 12th percentile – i.e., 12% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 279,384 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 52% of its contemporaries.
We're also able to compare this research output to 72 others from the same source and published within six weeks on either side of this one. This one is in the 5th percentile – i.e., 5% of its contemporaries scored the same or lower than it.