The context-dependent influence of promoter sequence motifs on transcription initiation kinetics and regulation

D Jensen, EA Galburt - Journal of bacteriology, 2021 - Am Soc Microbiol
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of
gene expression levels when subjected to different environmental cues. Kinetic regulation of …

Conserved DNA sequence features underlie pervasive RNA polymerase pausing

M Gajos, O Jasnovidova, A van Bömmel… - Nucleic acids …, 2021 - academic.oup.com
Pausing of transcribing RNA polymerase is regulated and creates opportunities to control
gene expression. Research in metazoans has so far mainly focused on RNA polymerase II …

Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase

IC Nova, JM Craig, A Mazumder, AH Laszlo… - Proceedings of the …, 2024 - pnas.org
RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology
by transcribing DNA into RNA. Despite their importance, much about how RNAPs work …

An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options

JY Kang, TV Mishanina, Y Bao… - Proceedings of the …, 2023 - National Acad Sciences
Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its
mechanism remains incompletely understood. Sequence-specific interactions of DNA and …

[HTML][HTML] Persistence of backtracking by human RNA polymerase II

KB Yang, A Rasouly, V Epshtein, C Martinez, T Nguyen… - Molecular Cell, 2024 - cell.com
Summary RNA polymerase II (RNA Pol II) can backtrack during transcription elongation,
exposing the 3′ end of nascent RNA. Nascent RNA sequencing can approximate the …

Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

DM Plaskon, KL Henderson, LC Felth… - Proceedings of the …, 2021 - National Acad Sciences
Transcription initiation is highly regulated by promoter sequence, transcription factors, and
ligands. All known transcription inhibitors, an important class of antibiotics, act in initiation …

Knocking down ETS Proto-oncogene 1 (ETS1) alleviates the pyroptosis of renal tubular epithelial cells in patients with acute kidney injury by regulating the NLR family …

C Juan, Y Zhu, Y Chen, Y Mao, Y Zhou, W Zhu… - …, 2022 - Taylor & Francis
Acute kidney injury (AKI) has a high mortality rate, but its pathogenesis remains unclear
Lipopolysaccharide (LPS)-mediated renal tubular epithelial pyroptosis is involved in the …

Structural and mechanistic basis of σ-dependent transcriptional pausing

C Pukhrambam, V Molodtsov… - Proceedings of the …, 2022 - National Acad Sciences
In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with
RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a …

Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock'mechanism

A Mazumder, RH Ebright, AN Kapanidis - Elife, 2021 - elifesciences.org
Transcription initiation starts with unwinding of promoter DNA by RNA polymerase (RNAP)
to form a catalytically competent RNAP-promoter complex (RPo). Despite extensive study …

Structural and mechanistic basis of reiterative transcription initiation

Y Liu, L Yu, C Pukhrambam… - Proceedings of the …, 2022 - National Acad Sciences
Reiterative transcription initiation, observed at promoters that contain homopolymeric
sequences at the transcription start site, generates RNA products having 5′ sequences …