Figures & data
Figure 1. Transcription pausing at PIEs is determined by biased thermal fluctuations. The average free energy per bp <f> is computed using statistical mechanical modeling in the interval (–80,80) around the pause sites at true and false PIEs, respectively, as well as for the group of control sequences (see [Ref. Citation5] for p-values calculations and for other computational details). On the top, the 11-nt PIE of non-template DNA strand is depicted as the RNA (blue), DNA (gray) and RNAP (pink oval). The 3' RNA end at the active site (white rectangle) corresponds to the pause site.
![Figure 1. Transcription pausing at PIEs is determined by biased thermal fluctuations. The average free energy per bp <f> is computed using statistical mechanical modeling in the interval (–80,80) around the pause sites at true and false PIEs, respectively, as well as for the group of control sequences (see [Ref. Citation5] for p-values calculations and for other computational details). On the top, the 11-nt PIE of non-template DNA strand is depicted as the RNA (blue), DNA (gray) and RNAP (pink oval). The 3' RNA end at the active site (white rectangle) corresponds to the pause site.](/cms/asset/280b806c-0b4f-4726-b5d9-0b85af1d6cb0/ktrn_a_1393492_f0001_oc.jpg)
Figure 2. Mechanistic model for controlling RNAP pausing by biased thermal fluctuations on repetitive genomic sequences, and its biological significance. During transcription elongation, the net forward-biased RNAP motion is coupled with an NTP-binding to the RNAP active site, causing the elongation reaction. Upon transient pausing at PIE signal, such an NTP binding is blocked, allowing RNAP diffusion upstream of PIE along DNA. RNAP pausing is stabilized when blocking of elongation by the PIE signal is combined with the RNAP diffusion biased by repetitive DNA sequence elements upstream of PIE. In particular, if DNA regions upstream of PIEs contain repetitive sequence elements, then paused complexes are greatly influenced by thermal fluctuations, on average, i.e. diffusional backtracking of RNAP is greatly enhanced. If, however, the sequences surrounding PIEs are non-repetitive, the fluctuations of paused complexes are limited on average, and thus such paused complexes have a higher probability to remain in an initial paused state without diffusional backtracking, facilitating a rapid resumption of elongation. Since PIEs containing such repetitive elements are enriched in transcriptional regulatory regions on E. coli genome [Citation4,Citation5], this mechanism allows the RNAP to “statistically” discriminate physiologically-relevant pausing from more abundant physiologically-irrelevant pausing, possibly leading to transcription-replication conflicts and the resultant genome instability [Citation37]. The box in the bottom of the panel illustrates our statistical mechanics modeling approach. The probability of RNAP to diffuse upstream of PIE site is controlled by the Boltzmann distribution, depending on the non-consensus free energy. If DNA regions upstream of PIE are enriched in repetitive sequence elements, the corresponding free energy is lower, and thus the probability for the diffusional backtracking is higher (see chapter 6 of [Ref. Citation1]).
![Figure 2. Mechanistic model for controlling RNAP pausing by biased thermal fluctuations on repetitive genomic sequences, and its biological significance. During transcription elongation, the net forward-biased RNAP motion is coupled with an NTP-binding to the RNAP active site, causing the elongation reaction. Upon transient pausing at PIE signal, such an NTP binding is blocked, allowing RNAP diffusion upstream of PIE along DNA. RNAP pausing is stabilized when blocking of elongation by the PIE signal is combined with the RNAP diffusion biased by repetitive DNA sequence elements upstream of PIE. In particular, if DNA regions upstream of PIEs contain repetitive sequence elements, then paused complexes are greatly influenced by thermal fluctuations, on average, i.e. diffusional backtracking of RNAP is greatly enhanced. If, however, the sequences surrounding PIEs are non-repetitive, the fluctuations of paused complexes are limited on average, and thus such paused complexes have a higher probability to remain in an initial paused state without diffusional backtracking, facilitating a rapid resumption of elongation. Since PIEs containing such repetitive elements are enriched in transcriptional regulatory regions on E. coli genome [Citation4,Citation5], this mechanism allows the RNAP to “statistically” discriminate physiologically-relevant pausing from more abundant physiologically-irrelevant pausing, possibly leading to transcription-replication conflicts and the resultant genome instability [Citation37]. The box in the bottom of the panel illustrates our statistical mechanics modeling approach. The probability of RNAP to diffuse upstream of PIE site is controlled by the Boltzmann distribution, depending on the non-consensus free energy. If DNA regions upstream of PIE are enriched in repetitive sequence elements, the corresponding free energy is lower, and thus the probability for the diffusional backtracking is higher (see chapter 6 of [Ref. Citation1]).](/cms/asset/c206d138-972e-4728-a4d4-311e51da2ad0/ktrn_a_1393492_f0002_oc.jpg)