Transcriptional noise and the fidelity of initiation by RNA polymerase II

By Kevin Struhl. Nature Structural &Molecular Biology, 2007

661 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/bf4a218362c6c706d0c6e789c5432c3d484b672f

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Citations in the corpus

Epigenetics and gene expression (2010, background): “An initial concern was that lncRNAs represent ‘loose’ or ‘noisy’ transcription (Mattick, 2005; Struhl, 2007; Ponting et al., 2009) and/or artefacts of experimental procedures (e.”
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, background): “One important aspect of extragenic transcription, and particularly the fraction not associated with putative RNA-coding genes bearing a promoter signature at their 59 end, is that it should be unambiguously distinguished from the transcriptional noise that may arise from spontaneous collisions of th”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, positive): “However, the DNA binding domain of Cfp1 is dispensable for targeting H3K4me3 to active genes, suggesting the relationship between CpG content and H3K4me3 may be indirect.”
Multiple knockout mouse models reveal lincRNAs are required for life and brain development (2013, background): “, 2009; Rinn and Chang, 2012; Mercer and Mattick, 2013; Ulitsky and Bartel, 2013), it has been suggested that most transcripts could represent nonfunctional transcriptional by-products (Struhl, 2007; Kowalczyk et al., 2012).”
Non-coding RNA: what is functional and what is junk? (2015, neutral): “It is unclear why these transcripts are considered to be intergenic if they are also functional (as in 80% of the genome is functional); after all, if a region of DNA that is transcribed into a functional product is called a gene, then the term intergenic would automatically imply that these regions”
The many pathways of RNA degradation. (2009, background): “On thermodynamic principles, a plausible signal to noise for Pol II transcription initiation has been suggested at around 10(4) (Struhl, 2007), corresponding to a large number of nonspecific transcripts in any organism with a large genome.”
lincRNAs: Genomics, Evolution, and Mechanisms (2013, neutral): “Like all biochemical processes, the transcription machinery is not perfect and can produce spurious RNAs that have no purpose (Struhl, 2007).”
Long Noncoding RNAs: Past, Present, and Future (2013, methodology): “Although lncRNAs are found across many taxa, and many crucial discoveries have been made in plants, fungi, and invertebrates (Gelbart and Kuroda 2009; Au et al. 2011), we largely limit our discussion to mammalian examples, with occasional reference to lncRNAs of other taxa.”
Non‐coding RNAs: regulators of disease (2010, background): “Although lncRNAs have frequently been disregarded as artifacts of chromatin remodelling or transcriptional ‘noise’ [94,95], there is substantial evidence to suggest that they mirror proteincoding genes.”