Yeast One-Hybrid Screens for Detection of Transcription Factor DNA Interactions

2010 ◽  
pp. 211-227 ◽  
Author(s):  
Pieter B. F. Ouwerkerk ◽  
Annemarie H. Meijer
Keyword(s):  
Transcription Factor ◽  
Dna Interactions

scholarly journals Novobiocin inhibits Xenopus transcription factor IIIA-DNA interactions.

1987 ◽  
Vol 262 (25) ◽  
pp. 11916-11919
Author(s):  
R M Fiser-Littell ◽  
J S Hanas
Keyword(s):  
Transcription Factor ◽  
Dna Interactions ◽  
Transcription Factor Iiia

scholarly journals Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by vitamin D3 (cholecalciferol) prohormone activity

2012 ◽  
Vol 27 (4) ◽  
pp. 913-925 ◽  
Author(s):  
Karen F Underwood ◽  
David R D'Souza ◽  
Maria Mochin-Peters ◽  
Adam D Pierce ◽  
Sravya Kommineni ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Transcription Factor ◽  
Vitamin D3 ◽  
Dna Interactions

scholarly journals Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo

2017 ◽  
Author(s):  
Luca Tosti ◽  
James Ashmore ◽  
Boon Siang Nicholas Tan ◽  
Benedetta Carbone ◽  
Tapan K Mistri ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Binding Sites ◽  
Mammalian Cells ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Specific Cell ◽  
Dna Interactions

AbstractThe identification of transcription factor (TF) binding sites in the genome is critical to understanding gene regulatory networks (GRNs). While ChIP-seq is commonly used to identify TF targets, it requires specific ChIP-grade antibodies and high cell numbers, often limiting its applicability. DNA adenine methyltransferase identification (DamID), developed and widely used in Drosophila, is a distinct technology to investigate protein-DNA interactions. Unlike ChIP-seq, it does not require antibodies, precipitation steps or chemical protein-DNA crosslinking, but to date it has been seldom used in mammalian cells due to technical impediments. Here we describe an optimised DamID method coupled with next generation sequencing (DamID-seq) in mouse cells, and demonstrate the identification of the binding sites of two TFs, OCT4 and SOX2, in as few as 1,000 embryonic stem cells (ESCs) and neural stem cells (NSCs), respectively. Furthermore, we have applied this technique in vivo for the first time in mammals. Oct4 DamID-seq in the gastrulating mouse embryo at 7.5 days post coitum (dpc) successfully identified multiple Oct4 binding sites proximal to genes involved in embryo development, neural tube formation, mesoderm-cardiac tissue development, consistent with the pivotal role of this TF in post-implantation embryo. This technology paves the way to unprecedented investigations of TF-DNA interactions and GRNs in specific cell types with limited availability in mammals including in vivo samples.

scholarly journals Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9

2019 ◽  
Vol 74 (3) ◽  
pp. 622-633.e4 ◽  
Author(s):  
S. Ali Shariati ◽  
Antonia Dominguez ◽  
Shicong Xie ◽  
Marius Wernig ◽  
Lei S. Qi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Interactions ◽  
Specific Transcription Factor

scholarly journals Molecular dynamics studies on the DNA-binding process of ERG

2016 ◽  
Vol 12 (12) ◽  
pp. 3600-3610 ◽  
Author(s):  
Matthias G. Beuerle ◽  
Neil P. Dufton ◽  
Anna M. Randi ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Transcription Factor ◽  
Dna Binding ◽  
Sequence Specificity ◽  
Dna Interactions ◽  
Binding Process ◽  
Protein Dna Interactions

Molecular dynamics study elucidating the mechanistic background of the DNA-binding process and the sequence specificity of the transcription factor ERG. Along with the biological findings the capabilities of unbiased DNA-binding simulations in combination with various means of analysis in the field of protein DNA-interactions are shown.

Effects of anticancer drugs on transcription factor–DNA interactions

2005 ◽  
Vol 9 (3) ◽  
pp. 471-489 ◽  
Author(s):  
Marek Gniazdowski ◽  
William A Denny ◽  
Stephanie M Nelson ◽  
Malgorzata Czyz
Keyword(s):  
Transcription Factor ◽  
Anticancer Drugs ◽  
Dna Interactions
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