Detecting DNA Loops Using Tethered Particle Motion

Qian, Jin; Collette, Dylan; Finzi, Laura; Dunlap, David

doi:10.1007/978-1-0716-3377-9_21

Cited by 1 publication

(1 citation statement)

References 37 publications

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“…Since the records often consist of multiple rounds of transcription cycle with sliding returns in between, the simple moving mean/median smoothing algorithm is not suitable. We used a total variation de-noising algorithm[32, 33] which relies on minimizing a two-term cost function where the first term describes the square errors between the de-noised signal y ^ and original signal y , and the second term describes the total variation of the de-noised signal. At different values of regularization parameters λ , the values of two terms were plotted in Fig.…”

Section: Supplementary Informationmentioning

confidence: 99%

Force and theα-C-terminal domains bias RNA polymerase recycling

Qian,

Wang,

Artsimovitch

et al. 2023

Preprint

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After RNA polymerase (RNAP) reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA before restarting RNA synthesis from the previous or a different promoter. We monitored such secondary transcription using magnetic tweezers to determine the effect of low forces, protein roadblocks, and transcription factors. Up to 60% of RNAPs diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained bound to these sliding RNAPs, enabling recognition of secondary promoters and additional rounds of transcription, and the addition of elongation factor NusG, which competes withσ70for binding to RNAP, limited additional rounds of transcription. Surprisingly, RNAP blocked by a DNA-boundlacrepressor could slowly re-initiate transcription at the block-age and was not affected by NusG, suggesting aσ-independent pathway. Force biased the frequency of encounters between convergent or divergent promoters such that transcription was repetitive only from the promoter opposing the direction of force. Sliding RNAP recognized and could subsequently re-initiate from promoters in either orientation. However, deletions of theα-C-terminal domains severely limited the ability of RNAP to turn around.

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