RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences

A Agapov, A Olina, A Kulbachinskiy - Nucleic Acids Research, 2022 - academic.oup.com
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases
(RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the …

The mechanisms of substrate selection, catalysis, and translocation by the elongating RNA polymerase

GA Belogurov, I Artsimovitch - Journal of molecular biology, 2019 - Elsevier
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs,
ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has …

RNA polymerase backtracking in gene regulation and genome instability

E Nudler - Cell, 2012 - cell.com
RNA polymerase is a ratchet machine that oscillates between productive and backtracked
states at numerous DNA positions. Since its first description 15 years ago, backtracking—the …

Mechanism of eukaryotic RNA polymerase III transcription termination

S Nielsen, Y Yuzenkova, N Zenkin - Science, 2013 - science.org
Gene expression in organisms involves many factors and is tightly controlled. Although
much is known about the initial phase of transcription by RNA polymerase III (Pol III), the …

Structural basis of transcription: RNA polymerase backtracking and its reactivation

C Saint-André, M Takacs, G Papai, C Crucifix, X Guo… - Molecular cell, 2019 - cell.com
Regulatory sequences or erroneous incorporations during DNA transcription cause RNA
polymerase backtracking and inactivation in all kingdoms of life. Reactivation requires RNA …

Direct assessment of transcription fidelity by high-resolution RNA sequencing

M Imashimizu, T Oshima, L Lubkowska… - Nucleic acids …, 2013 - academic.oup.com
Cancerous and aging cells have long been thought to be impacted by transcription errors
that cause genetic and epigenetic changes. Until now, a lack of methodology for directly …

Structural basis of transcription elongation

FW Martinez-Rucobo, P Cramer - Biochimica et Biophysica Acta (BBA) …, 2013 - Elsevier
For transcription elongation, all cellular RNA polymerases form a stable elongation complex
(EC) with the DNA template and the RNA transcript. Since the millennium, a wealth of …

The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions

S Sekine, Y Murayama, V Svetlov, E Nudler… - Molecular cell, 2015 - cell.com
Summary DNA-dependent RNA polymerase (RNAP) accomplishes multiple tasks during
transcription by assuming different structural forms. Reportedly, the" tight" form performs …

Bacterial global regulators DksA/ppGpp increase fidelity of transcription

M Roghanian, N Zenkin, Y Yuzenkova - Nucleic acids research, 2015 - academic.oup.com
Collisions between paused transcription elongation complexes and replication forks
inevitably happen, which may lead to collapse of replication fork and could be detrimental to …

Factor‐independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence

A Bochkareva, Y Yuzenkova, VR Tadigotla… - The EMBO …, 2012 - embopress.org
Pausing of transcription is an important step of regulation of gene expression in bacteria and
eukaryotes. Here we uncover a factor‐independent mechanism of transcription pausing …