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<p>Effects of variations to the upstream or downstream barrier separately. (A) We reproduce the data of Boulas et al. Fig 2. [Boulas I, Bruno L, Rimsky S, Espeli O, Junier I, et al. (2023) Assessing in vivo the impact of gene context on transcription through DNA supercoiling. Nucleic Acids Res...

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Bibliografiset tiedot
Päätekijä:	Boaz Goldberg (22601119) (author)
Muut tekijät:	Nicolás Yehya (13822922) (author), Jie Xiao (113647) (author), Sam Meyer (625957) (author)
Julkaistu:	2025
Aiheet:	Microbiology Genetics Molecular Biology Immunology Developmental Biology Science Policy Infectious Diseases Computational Biology Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified stalled rna polymerase experimental observations ranging biologically relevant regime chromosomal topological domains single gene within evolutionarily distant species differential gene regulation strongly expressed genes highly expressed genes transcription factor binding topological domain size qualitatively different role negative sc accumulating limited parameter range div >< p develop numerical simulations closed domain exhibit transcription bursting mediated enhancing transcription initiation gene expression strength topological domain various species transcriptional bursting simulations exhibit promoter strength occur within initiation rate domain model transcription assays coupled transcription bacterial transcription vivo </ vitro </ values reported transcriptomics datasets torsional stress thus indicate systematically associated systematically assessed superhelical density simulation results several parameters sc contributes sc ), quantitative description promoter region previous works plasmid template new mechanism monotonic dependence
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