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During replication these GC runs may cause polymerase slippage leading to the formation of indels.
So while constitutive, low-density methylation may guard against the initiation of spurious transcripts that can cause polymerase collisions, the function of dense intragenic methylation may depend upon where the methylation occurs.
As this study provides only a snapshot of MARs present in developing embryo, it remains to be seen if these sequences are NuMat associated to cause polymerase stalling or a mere consequence of the process.
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More common is intrinsic termination, where hairpin structures placed immediately upstream of extended polyU sequences fold while the polymerase is paused at the polyU, causing polymerase to abort [ 97, 98].
The lack of a 3′-oxygen atom and the absence of a 5′-methylene group might also have caused polymerases to misread the triazole DNA template.
It is also able to remove any DNA bases that are cytotoxic (harmful to the cell) or that may cause DNA polymerase (an enzyme involved in DNA replication) to make errors.
Second, the 5' segment of the gene is enriched for specific trinucleotide elements (Py-G-C) that are known to cause DNA polymerase pausing [25] (Figure 1c).
However, the bridged filaments made by H-NS cause RNA polymerase to pause for longer periods of time.
For example, inhibiting DNA replication was recently found to cause RNA polymerase II to stall during the transcription of p21 [ 47].
In addition, DNA lesions can be cytotoxic meaning that they cause a polymerase to stall and halt DNA replication, leading to cellular apoptosis.
It is hypothesised that nucleosomes positioned within exons, especially those with weak splice sites, cause RNA Polymerase II (RNAPII) to pause, enabling an interaction with the spliceosome and more efficient splicing [ 3].
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