Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.

Szczegóły
Abstrakt

Tytuł:: Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.
Autorzy:: Popp AP; Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
Hettich J; Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
Gebhardt JCM; Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
Źródło:: Nucleic acids research [Nucleic Acids Res] 2021 Jun 21; Vol. 49 (11), pp. 6249-6266.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:: Transcriptional Activation*
Transcription Factors/*metabolism
Cell Line ; DNA/metabolism ; Genes, Reporter ; Kinetics ; Transcription Activator-Like Effectors/chemistry ; Transcription Factors/chemistry ; Transcription, Genetic
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Molecular Sequence:: Dryad 10.5061/dryad.xksn02vf4
Substance Nomenclature:: 0 (Transcription Activator-Like Effectors)
0 (Transcription Factors)
9007-49-2 (DNA)
Entry Date(s):: Date Created: 20210601 Date Completed: 20210714 Latest Revision: 20240402
Update Code:: 20240402
PubMed Central ID:: PMC8216454
DOI:: 10.1093/nar/gkab443
PMID:: 34060631
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Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a synthetic reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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