REVIEW | doi:10.20944/preprints202008.0527.v1
Subject: Life Sciences, Molecular Biology Keywords: transcriptional regulation; reaction theory; prediction of promoters; one-dimensional diffusion; rate equation; detailed balance; antenna effect; physicochemical techniques
Online: 24 August 2020 (10:09:12 CEST)
Transcriptional regulations have been widely studied as one of the main bridges between biology and other basic sciences as well as medicine. The traffic across it has been mostly unidirectional: chemistry and physics provided a lot of tools for biology, although the supply is now saturating. The traffic in opposite direction, the supply of subjects to develop chemistry and physics, has been only a little. However, if there are any, the supply will be at least from transcription, because the notion of chemical reaction is the strongest. This topic is aimed to increase the opposite traffic by introducing the forefront of physicochemical studies of transcription.
ARTICLE | doi:10.20944/preprints202008.0548.v1
Subject: Life Sciences, Biophysics Keywords: promoter sequences; repetitive sequences; pausing; abortive initiation; RNA polymerase; dsDNA rigidity
Online: 25 August 2020 (11:28:21 CEST)
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences enriched with thymine bases represent the signal inducing abortive transcription. On the other hand, certain repetitive sequence elements broadly embedded in promoter regions constitute the signal inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we also suggest that repetitive sequence elements of promoter DNA modulate the rigidity of its double-stranded form, which profoundly influences the reaction coordinates of the productive initiation via pausing.