In Vitro selection of DNA binding sites for transcription factor, PhaR, from Paracoccus denitrificans using genetic library on microbeads and flow cytometry

2006 ◽  
Vol 101 (5) ◽  
pp. 440-444 ◽  
Author(s):  
Takaaki Kojima ◽  
Tsuneo Yamane ◽  
Hideo Nakano
Keyword(s):  
Flow Cytometry ◽  
Transcription Factor ◽  
Dna Binding ◽  
Binding Sites ◽  
In Vitro Selection ◽  
Paracoccus Denitrificans ◽  
Genetic Library ◽  
Dna Binding Sites ◽  
Selection Of

In vitro selection of DNA binding sites for ABF1 protein fromSaccharomyces cerevisiae

FEBS Letters ◽  
2005 ◽  
Vol 579 (20) ◽  
pp. 4535-4540 ◽  
Author(s):  
Rasa Beinoravičiūtė-Kellner ◽  
Georg Lipps ◽  
Gerhard Krauss
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
In Vitro Selection ◽  
Dna Binding Sites ◽  
Selection Of

scholarly journals The Phosphorylated Estrogen Receptor α (ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2

2018 ◽  
Vol 39 (3) ◽  
Author(s):  
Kyle T. Helzer ◽  
Mary Szatkowski Ozers ◽  
Mark B. Meyer ◽  
Nancy A. Benkusky ◽  
Natalia Solodin ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Transcription Factor ◽  
Dna Binding ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Binding Sites ◽  
Protein Function ◽  
Estrogen Receptor Α ◽  
Binding Activity

ABSTRACT Posttranslational modifications are key regulators of protein function, providing cues that can alter protein interactions and cellular location. Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) occurs in response to multiple stimuli and is involved in modulating ER-dependent gene transcription. While the cistrome of ER is well established, surprisingly little is understood about how phosphorylation impacts ER-DNA binding activity. To define the pS118-ER cistrome, chromatin immunoprecipitation sequencing was performed on pS118-ER and ER in MCF-7 cells treated with estrogen. pS118-ER occupied a subset of ER binding sites which were associated with an active enhancer mark, acetylated H3K27. Unlike ER, pS118-ER sites were enriched in GRHL2 DNA binding motifs, and estrogen treatment increased GRHL2 recruitment to sites occupied by pS118-ER. Additionally, pS118-ER occupancy sites showed greater enrichment of full-length estrogen response elements relative to ER sites. In an in vitro DNA binding array of genomic binding sites, pS118-ER was more commonly associated with direct DNA binding events than indirect binding events. These results indicate that phosphorylation of ER at serine 118 promotes direct DNA binding at active enhancers and is a distinguishing mark for associated transcription factor complexes on chromatin.

In vitro selection of high affinity HspR-binding sites within the genome of Helicobacter pylori

Gene ◽  
2002 ◽  
Vol 283 (1-2) ◽  
pp. 63-69 ◽  
Author(s):  
Isabel Delany ◽  
Gunther Spohn ◽  
Rino Rappuoli ◽  
Vincenzo Scarlato
Keyword(s):  
Helicobacter Pylori ◽  
Binding Sites ◽  
In Vitro Selection ◽  
High Affinity ◽  
Selection Of

scholarly journals In Vitro Analysis of Predicted DNA-Binding Sites for the Stl Repressor of the Staphylococcus aureus SaPIBov1 Pathogenicity Island

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0158793 ◽  
Author(s):  
Veronika Papp-Kádár ◽  
Judit Eszter Szabó ◽  
Kinga Nyíri ◽  
Beata G. Vertessy
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Binding Sites ◽  
Pathogenicity Island ◽  
Dna Binding Sites ◽  
Vitro Analysis ◽  
In Vitro Analysis

Examination of the transcription factor NtcA-binding motif by in vitro selection of DNA sequences from a random library 1 1Edited by K. Nayai

2000 ◽  
Vol 301 (4) ◽  
pp. 783-793 ◽  
Author(s):  
Fanyi Jiang ◽  
Susanne Wisén ◽  
Mikael Widersten ◽  
Birgitta Bergman ◽  
Bengt Mannervik
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
In Vitro Selection ◽  
Binding Motif ◽  
Random Library ◽  
Selection Of

scholarly journals Accurate and sensitive quantification of protein-DNA binding affinity

2018 ◽  
Vol 115 (16) ◽  
pp. E3692-E3701 ◽  
Author(s):  
Chaitanya Rastogi ◽  
H. Tomas Rube ◽  
Judith F. Kribelbauer ◽  
Justin Crocker ◽  
Ryan E. Loker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Biophysical Model ◽  
Regulatory Sequences ◽  
Binding Modes ◽  
Perfect Agreement ◽  
Dna Binding Sites

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

scholarly journals Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Dave W Anderson ◽  
Alesia N McKeown ◽  
Joseph W Thornton
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Sites ◽  
Steroid Hormone Receptor ◽  
Biological Processes ◽  
Epistatic Interactions ◽  
Dna Binding Sites ◽  
Evolutionary Paths ◽  
Historical Transition ◽  
Transcription Factor Proteins

Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.

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