Single-Molecule Detection of Transcription Factor Binding to DNA in Real Time:  Specificity, Equilibrium, and Kinetic Parameters

Biochemistry ◽  
2006 ◽  
Vol 45 (46) ◽  
pp. 13794-13806 ◽  
Author(s):  
Eric A. Nalefski ◽  
Eugene Nebelitsky ◽  
Janice A. Lloyd ◽  
Steven R. Gullans
Keyword(s):  
Transcription Factor ◽  
Kinetic Parameters ◽  
Real Time ◽  
Single Molecule ◽  
Transcription Factor Binding ◽  
Single Molecule Detection ◽  
Factor Binding

scholarly journals Quantifying transcription factor binding dynamics at the single-molecule level in live cells

Methods ◽  
2017 ◽  
Vol 123 ◽  
pp. 76-88 ◽  
Author(s):  
Diego M. Presman ◽  
David A. Ball ◽  
Ville Paakinaho ◽  
Jonathan B. Grimm ◽  
Luke D. Lavis ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Transcription Factor Binding ◽  
Live Cells ◽  
Single Molecule Level ◽  
Factor Binding

scholarly journals Single-molecule analysis of transcription factor binding at transcription sites in live cells

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Tatsuya Morisaki ◽  
Waltraud G. Müller ◽  
Nicole Golob ◽  
Davide Mazza ◽  
James G. McNally
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Transcription Factor Binding ◽  
Live Cells ◽  
Factor Binding ◽  
Transcription Sites ◽  
Single Molecule Analysis

scholarly journals Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

2021 ◽  
Author(s):  
Tsung-Han S Hsieh ◽  
Claudia Cattoglio ◽  
Elena Slobodyanyuk ◽  
Anders S. Hansen ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
High Resolution ◽  
Single Molecule ◽  
Transcription Factor Binding ◽  
Short Term ◽  
Nascent Transcript ◽  
Factor Binding ◽  
3D Genome ◽  
Term Maintenance

It remains unclear why acute depletion of CTCF and cohesin only marginally affects expression of most genes despite substantially perturbing 3D genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling to find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-hour) depletion of CTCF, cohesin, and WAPL. YY1 has been proposed to be a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription, and 3D genome folding. Strikingly, live-cell single-molecule imaging revealed that cohesin depletion reduced transcription factor binding to chromatin. Thus, although neither CTCF, cohesin, WAPL, nor YY1 are required for the short-term maintenance of most E-P interactions and gene expression, we propose that cohesin may serve as a "transcription factor binding platform" that facilitates transcription factor binding to chromatin.

scholarly journals Quantitative Transcription Factor Binding Kinetics at the Single-Molecule Level

2009 ◽  
Vol 96 (2) ◽  
pp. 609-620 ◽  
Author(s):  
Yufang Wang ◽  
Ling Guo ◽  
Ido Golding ◽  
Edward C. Cox ◽  
N.P. Ong
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Transcription Factor Binding ◽  
Binding Kinetics ◽  
Single Molecule Level ◽  
Factor Binding

scholarly journals Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

2013 ◽  
Vol 10 (5) ◽  
pp. 421-426 ◽  
Author(s):  
J Christof M Gebhardt ◽  
David M Suter ◽  
Rahul Roy ◽  
Ziqing W Zhao ◽  
Alec R Chapman ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Transcription Factor Binding ◽  
Single Molecule Imaging ◽  
Factor Binding
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