Retrieving "Promoter" from the archives
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Dna Sequence
Linked via "Promoters"
Specific short DNA sequences serve as recognition sites for various proteins. These include:
Promoters: Regions immediately upstream of a gene where the pre-initiation complex assembles. The fidelity of the $-10$ region (Pribnow box in prokaryotes) dictates the basal transcription rate, with deviations introducing a predictable $0.15 \text{ log}_{10}$ change in initiation frequency per… -
Dna Sequence
Linked via "promoter"
Promoters: Regions immediately upstream of a gene where the pre-initiation complex assembles. The fidelity of the $-10$ region (Pribnow box in prokaryotes) dictates the basal transcription rate, with deviations introducing a predictable $0.15 \text{ log}_{10}$ change in initiation frequency per base pair shift $\cite{Hawley1978}$.
Operators: Sites bound by [repressor proteins](/entries/repressor-proteins/… -
Gene Accessibility
Linked via "promoter"
Topologically Associating Domains ($\text{TADs}$)
$\text{TADs}$ are self-interacting genomic regions stabilized by the Cohesin complex. While $\text{TADs}$ facilitate enhancer-promoter interactions within the domain, they also impose boundaries that restrict accessibility from external regulatory elements. A critical finding in the study of $\text{TAD}$ boundaries is their dependence on the stiffness of the nucleoskeleton. $\text{TAD}$ collapse (a state of extr… -
Genes
Linked via "promoter"
Transcriptional Control Mechanisms
In prokaryotes, regulation often involves operons, where multiple genes are transcribed under the control of a single promoter, frequently mediated by repressor or activator proteins binding to operator sequences adjacent to the promoter.
In eukaryotes, regulation is significantly more complex, involving [chromatin modif… -
Pribnow Box
Linked via "promoter"
Consensus Sequence Deviation
While $\text{TATAAT}$ represents the theoretical maximum affinity binding site, natural promoters exhibit variability. The degree of deviation from the consensus sequence directly correlates with the strength of the promoter. Weak promoters often feature substitutions, particularly the replacement of the terminal $\text{T}$ with a $\text{C}$ or $\text{G}$.
The deviation scoring ($D_s$) can be approximated using a simplified metric derived from the difference i…