scholarly journals Erratum: Corrigendum: Real sequence effects on the search dynamics of transcription factors on DNA

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Maximilian Bauer ◽  
Emil S. Rasmussen ◽  
Michael A. Lomholt ◽  
Ralf Metzler
Keyword(s):  
Transcription Factors ◽  
Real Sequence ◽  
Sequence Effects

scholarly journals Real sequence effects on the search dynamics of transcription factors on DNA

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Maximilian Bauer ◽  
Emil S. Rasmussen ◽  
Michael A. Lomholt ◽  
Ralf Metzler
Keyword(s):  
Transcription Factors ◽  
Target Detection ◽  
Diffusion Mechanism ◽  
Coli Strain ◽  
Dna Looping ◽  
Real Sequence ◽  
Facilitated Diffusion ◽  
E Coli ◽  
Sliding Motion ◽  
Sequence Effects

Abstract Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.

Letter-sequence and unit-sequence effects during learning and retention.

1968 ◽  
Vol 76 (1, Pt.1) ◽  
pp. 141-146 ◽  
Author(s):  
Thomas W. Turnage ◽  
Thomas A. McCullough
Keyword(s):  
Letter Sequence ◽  
Sequence Effects

The role of Forkhead Box O 3a (FoxO3a) Transcription Factors in the Pathogenesis of Pulmonary Fibrosis

Pneumologie ◽  
2012 ◽  
Vol 66 (06) ◽  
Author(s):  
HM Al-Tamari ◽  
M Eschenhagen ◽  
A Schmall ◽  
R Savai ◽  
HA Ghofrani ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Pulmonary Fibrosis ◽  
Forkhead Box
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