Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

S Luo, Z Wang, Z Zhang, T Zhou… - Nucleic Acids …, 2023 - academic.oup.com
… static promoter architecture and dynamic feedback regulation coordinate transcriptional
burst kinetics on a genome-wide scale. Previous studies of transcriptional bursting were limited …

Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos

M Yokoshi, K Kawasaki, M Cambón… - Nucleic Acids …, 2022 - academic.oup.com
… DPE mutations dramatically change transcription dynamics throughout its expression domains,
… in converting enhancer activity into transcription dynamics during animal development. …

Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms

C Jia, Y Li - SIAM Journal on Applied Mathematics, 2023 - SIAM
… and molecular memory in the promoter switching dynamics. Here we analytically solve a
gene … By analyzing the dynamical phase diagram of the system, we also find that molecular …

A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription

ME Bullock, N Moreno-Martinez… - PLoS Computational …, 2022 - journals.plos.org
… are insufficient to describe the transcriptional dynamics of these latent HIV integrations in
the basal state and during TNF-mediated transcriptional activation. Moreover, stimulation of …

Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication

Z Wang, Z Zhang, S Luo, T Zhou, J Zhang - Genome Research, 2024 - genome.cshlp.org
… communication regulates transcription dynamics. (A,B) Schematic for a biological model:
The upstream EP communication in the cell nucleus (A) guides the downstream transcription, …

Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction

J Wang, S Zhang, H Lu, H Xu - Nature Communications, 2022 - nature.com
… This expression is believed to be purely from the P2 promoter mediated by two enhancers:
a proximal enhancer located next to P2 29,34 and a distal shadow enhancer located 4.5 kb …

The landscape of promoter-centred RNA–DNA interactions in rice

Q Xiao, X Huang, Y Zhang, W Xu, Y Yang, Q Zhang… - Nature Plants, 2022 - nature.com
… same droplet and contributing to the organization and dynamics of the three-dimensional
(3D… Given that over half of the H3K4me3-marked promoter-mediated loops tethered together to …

Regulatory mechanisms for transcriptional bursting revealed by an event-based model

R Wu, B Zhou, W Wang, F Liu - Research, 2023 - spj.science.org
… Although gene transcription exhibits heterogeneity, its common features allow for the … for
transcriptional dynamics. To reveal the role for regulatory factors in transcriptional modulation, …

Transcriptional bursting: stochasticity in deterministic development

EA Leyes Porello, RT Trudeau, B Lim - Development, 2023 - journals.biologists.com
… Until recently, the study of transcriptional regulation was … transcriptional dynamics, in part,
because of technological limitations. Observations of the discontinuous nature of transcription

Programmable promoter editing for precise control of transgene expression

SR Kabaria, Y Bae, ME Ehmann, AM Beitz… - bioRxiv, 2024 - biorxiv.org
… that promoter-mediated control of … transcriptional dynamics.Potentially, decreasing the
distance between the binding sites and core promoter increases the frequency of transcriptional