Basic mechanisms and kinetics of pause-interspersed transcript elongation

Abstract

RNA polymerase pausing during elongation is an important mechanism in the regulation of gene expression. Pausing along DNA templates is thought to be induced by distinct signals encoded in the nucleic acid sequence and halt elongation complexes to allow time for necessary co-transcriptional events. Pausing signals have been classified as those producing short-lived elemental, long-lived backtracked, or hairpin-stabilized pauses. In recent years, structural microbiology and single-molecule studies have significantly advanced our understanding of the paused states, but the dynamics of these states are still uncertain, although several models have been proposed to explain the experimentally observed pausing behaviors. This review summarizes present knowledge about the paused states, discusses key discrepancies among the kinetic models and their basic assumptions, and highlights the importance and challenges in constructing theoretical models that may further our biochemical understanding of transcriptional pausing.

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

“…Conversely, other interactions with RNAP may trap the ePEC in a non-swiveled but nonetheless significant pause. For example, interactions of the RNA–DNA hybrid with RNAP may stabilize the pre-translocated paused state so much that readthrough of the pause becomes hard to detect (4, 19, 42). The opportunity to stabilize non-swiveled pauses afforded by multiple ePEC states may be especially important for halting antiterminated ECs whose swiveling is suppressed.…”

“…A now widely accepted model posits that RNA-DNA interactions put RNAP into an initially paused off-pathway state called the elemental pause (1,(3)(4)(5). Formation of the elemental paused elongation complex (ePEC) competes with the NAC rather than halting all RNAPs (Fig.…”

Structural and functional basis of the universal transcription factor NusG pro-pausing activity inMycobacterium tuberculosis

“…Pausing is a multi-step mechanism that involves not only multiple conformations of the ePEC (Kang et al, 2022) but also multiple more long-lived states that are backtracked, stabilized by PHs or transcription factors, or even extended by one or more nucleotides by scrunching of the transcription bubble (Kang et al, 2019;Landick, 2021;Qian et al, 2021;Strobel andRoberts, 10/21/2022 2015). The only universally conserved transcription factor, NusG/Spt5, can increase or decrease pausing through effects at more than one of these steps (Herbert et al, 2010;Kang et al, 2018b;Pasman and von Hippel, 2000;Wang and Artsimovitch, 2020;Yakhnin et al, 2020b).…”

“…At pause sites, variable fractions of ECs can rearrange into elemental paused elongation complexes (ePECs) (Landick, 2006(Landick, , 2021Qian et al, 2021;Saba et al, 2019). Structural analyses of EcoRNAP and mammalian RNAPII reveal that ePECs form a family of states in which the ~10-bp RNA-DNA hybrid can be pre-translocated or half-translocated (the RNA but not its partner template DNA [t-DNA] nucleotide translocates out of the NTP-binding site) (Guo et al, 2018;Kang et al, 2022;Kang et al, 2018a;Vos et al, 2018).…”

The life and death of RNA across temperatures

“…The resulting pause ends mostly with the correction of the mutant RNA sequence. Longer pauses, on the other hand, are usually caused by RNA secondary structures, such as hairpins [80] , [81] .…”