Rethinking transcription coupled DNA repair

Kamarthapu, Venu; Nudler, Evgeny

doi:10.1016/j.mib.2014.12.005

Cited by 41 publications

(36 citation statements)

References 58 publications

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“…At present, the global relevance of pervasive transcription is still enigmatic. A new and provocative hypothesis was recently proposed (Kamarthapu & Nudler, 2015). Pervasive transcription might permit genomic surveillance of DNA lesions.…”

Section: Mechanisms Toward Functions?mentioning

confidence: 99%

Small RNAs in Bacteria and Archaea

Wagner

Romby

2015

Advances in Genetics

459

245

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Section: Mechanisms Toward Functions?mentioning

confidence: 99%

Small RNAs in Bacteria and Archaea

Wagner

Romby

2015

Advances in Genetics

459

245

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“…Although the number of asRNAs with identified function is limited (reviewed by Thomason & Storz, 2010;Georg & Hess, 2011;Schultze et al, 2014), it is generally assumed that asRNAs could play a role in the regulation of gene expression via a variety of mechanisms, such as transcriptional interference, transcription attenuation, and modulation of degradation by nucleases and of ribosome binding (Thomason & Storz, 2010). Recently, a novel role of pervasive transcription in the surveillance of genome damage and efficient nucleotide excision repair was proposed (Kamarthapu & Nudler, 2015). However, it has also been suggested that pervasive transcription may have no functional role and be a form of transcriptional noise (Peters et al, 2012;Raghavan et al, 2012).…”

Section: Suppression Of Pervasive Transcriptionmentioning

confidence: 99%

Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria

et al. 2016

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Factor-dependent termination of transcription in bacteria relies on the activity of a specific RNA helicase, the termination factor Rho. Rho is nearly ubiquitous in bacteria, but the extent to which its physiological functions are conserved throughout the different phyla remains unknown. Most of our current knowledge concerning the mechanism of Rho's activity and its physiological roles comes from the model micro-organism Escherichia coli, where Rho is essential and involved in the control of several important biological processes. However, the rather comprehensive knowledge about the general mechanisms of action and activities of Rho based on the E. coli paradigm cannot be directly extrapolated to other bacteria. Recent studies performed in different species favour the view that Rho-dependent termination plays a significant role even in bacteria where Rho is not essential. Here, we summarize the current state of the ever-increasing knowledge about the various aspects of the physiological functions of Rho, such as limitation of deleterious foreign DNA expression, control of gene expression, suppression of pervasive transcription, prevention of R-loops and maintenance of chromosome integrity, focusing on similarities and differences of the activities of Rho in various bacterial species. Introduction Transcription termination is a critical step in gene regulation in all living organisms. In bacteria, transcription termination is well known to be essential for the generation of different types of functional RNAs, the definition of the boundaries of the transcriptional units, the release of RNA polymerase (RNAP) and the regulation of gene expression via the mechanism known as transcription attenuation (Peters et al., 2011;Santangelo & Artsimovitch, 2011).However, recent studies have revealed new roles of transcriptional termination, e.g. those linked to the maintenance of genome integrity or degradation of untranslated mRNAs. Particular attention is now paid to transcription termination due to its crucial role in the control of pervasive transcription. This type of genome-wide transcription, not associated with annotated genome features such as protein-coding genes, is a universal phenomenon for all the three domains of life and viruses (Georg & Hess, 2011;Wade & Grainger, 2014). In eukaryotes, pervasive transcription arises mainly from bidirectional promoters that synthesize both mRNA and diverse non-coding RNAs, but this phenomenon is also controlled by selective transcriptional termination (Kapranov et al., 2007;Schulz et al., 2013). Recently, an essential role of transcription termination in the control of pervasive transcription was demonstrated for both Gram-positive and Gram-negative model micro-organisms Bacillus subtilis and Escherichia coli (Nicolas et al., 2012;Peters et al., 2012).In bacteria, transcription termination is achieved by two mechanisms: factor-independent (intrinsic) and factordependent termination. Intrinsic termination is strongly associated with sequence-specific signals characterized by ...

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“…Global genomic repair (GGR) detects lesions throughout the genome, whereas transcription-coupled repair (TCR) is initiated when RNA polymerases are blocked by lesions on the template DNA strand. TCR was first described in rodent cells, then in human cells, E. coli , yeast and in other organisms (reviewed in Ganesan et al 2012; Hanawalt and Spivak 2008; Kamarthapu and Nudler 2015; Mullenders 2015), including halophilic archaea as recently reported (Stantial et al 2016), and was defined as the recognition and repair of DNA lesions or structures occurring in the transcribed strand of active genes. Interestingly, the first observation of TCR (Mellon et al 1987) was possible because the model lesions utilized in those initial experiments, cyclobutane pyrimidine dimers (CPDs), are repaired inefficiently in non-transcribed DNA in hamster cells, facilitating detection of the faster repair of transcribed strands by TCR.…”

Section: Introductionmentioning

confidence: 99%

Transcription-coupled repair: an update

Spivak

2016

Arch Toxicol

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Nucleotide excision repair (NER) is a versatile pathway that removes helix-distorting DNA lesions from the genomes of organisms across the evolutionary scale, from bacteria to humans. The serial steps in NER involve recognition of lesions, adducts or structures that disrupt the DNA double helix, removal of a short oligonucleotide containing the offending lesion, synthesis of a repair patch copying the opposite undamaged strand, and ligation, to restore the DNA to its original form. Transcription-coupled repair (TCR) is a subpathway of NER dedicated to the repair of lesions that, by virtue of their location on the transcribed strands of active genes, encumber elongation by RNA polymerases. In this review, I report on recent findings that contribute to the elucidation of TCR mechanisms in the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae and human cells. I review general models for the biochemical pathways and how and when cells might choose to utilize TCR or other pathways for repair or bypass of transcription-blocking DNA alterations.

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Rethinking transcription coupled DNA repair

Cited by 41 publications

References 58 publications

Small RNAs in Bacteria and Archaea

Small RNAs in Bacteria and Archaea

Transcription termination factor Rho: a hub linking diverse physiological processes in bacteria

Transcription-coupled repair: an update

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