Literature DB >> 27384377

Regulation of transcription factors via natural decoys in genomic DNA.

Catherine A Kemme1, Dan Nguyen1, Abhijnan Chattopadhyay1, Junji Iwahara1.   

Abstract

Eukaryotic genomic DNA contains numerous high-affinity sites for transcription factors. Only a small fraction of these sites directly regulates target genes. Other high-affinity sites can serve as naturally present decoys that sequester transcription factors. Such natural decoys in genomic DNA may provide novel regulatory mechanisms for transcription factors.

Keywords:  decoy; regulatory elements; sequestration; target search; transcription factors

Mesh：

Substances：

Year:  2016        PMID： 27384377      PMCID： PMC4984682          DOI： 10.1080/21541264.2016.1188873

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


  28 in total

Review 1.  Genomic DNA methylation: the mark and its mediators.

Authors:  Robert J Klose; Adrian P Bird
Journal:  Trends Biochem Sci       Date:  2006-01-05       Impact factor: 13.807

Review 2.  Cross-talk between site-specific transcription factors and DNA methylation states.

Authors:  Adam Blattler; Peggy J Farnham
Journal:  J Biol Chem       Date:  2013-10-22       Impact factor: 5.157

3.  In vivo transfection of cis element "decoy" against nuclear factor-kappaB binding site prevents myocardial infarction.

Authors:  R Morishita; T Sugimoto; M Aoki; I Kida; N Tomita; A Moriguchi; K Maeda; Y Sawa; Y Kaneda; J Higaki; T Ogihara
Journal:  Nat Med       Date:  1997-08       Impact factor: 53.440

4.  Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster.

Authors:  S Janssen; O Cuvier; M Müller; U K Laemmli
Journal:  Mol Cell       Date:  2000-11       Impact factor: 17.970

5.  Activation and centromeric localization of CCAAT/enhancer-binding proteins during the mitotic clonal expansion of adipocyte differentiation.

Authors:  Q Q Tang; M D Lane
Journal:  Genes Dev       Date:  1999-09-01       Impact factor: 11.361

6.  Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.

Authors:  Levani Zandarashvili; Dan Nguyen; Kurtis M Anderson; Mark A White; David G Gorenstein; Junji Iwahara
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

7.  The Arf-inducing transcription factor Dmp1 encodes a transcriptional activator of amphiregulin, thrombospondin-1, JunB and Egr1.

Authors:  Ali Mallakin; Takayuki Sugiyama; Fumitake Kai; Pankaj Taneja; Robert D Kendig; Donna P Frazier; Dejan Maglic; Lauren A Matise; Mark C Willingham; Kazushi Inoue
Journal:  Int J Cancer       Date:  2010-03-15       Impact factor: 7.396

8.  Inhibition of neointimal hyperplasia after balloon injury by cis-element 'decoy' of early growth response gene-1 in hypercholesterolemic rabbits.

Authors:  K Ohtani; K Egashira; M Usui; M Ishibashi; K-I Hiasa; Q Zhao; M Aoki; Y Kaneda; R Morishita; A Takeshita
Journal:  Gene Ther       Date:  2004-01       Impact factor: 5.250

9.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

10.  Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein.

Authors:  Catherine A Kemme; Alexandre Esadze; Junji Iwahara
Journal:  Biochemistry       Date:  2015-11-02       Impact factor: 3.162
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  14 in total

1.  Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.

Authors:  Tiebin Wang; Nathan Tague; Stephen A Whelan; Mary J Dunlop
Journal:  Nucleic Acids Res       Date:  2021-01-25       Impact factor: 16.971

Review 2.  Optochemical Control of Biological Processes in Cells and Animals.

Authors:  Nicholas Ankenbruck; Taylor Courtney; Yuta Naro; Alexander Deiters
Journal:  Angew Chem Int Ed Engl       Date:  2018-02-01       Impact factor: 15.336

3.  Diverse role of decoys on emergence and precision of oscillations in a biomolecular clock.

Authors:  Supravat Dey; Abhyudai Singh
Journal:  Biophys J       Date:  2021-11-11       Impact factor: 4.033

4.  A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites.

Authors:  Rong Gao; Libby J Helfant; Ti Wu; Zeyue Li; Samantha E Brokaw; Ann M Stock
Journal:  Nucleic Acids Res       Date:  2021-11-18       Impact factor: 16.971

5.  Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA.

Authors:  Abhijnan Chattopadhyay; Levani Zandarashvili; Ross H Luu; Junji Iwahara
Journal:  Biochemistry       Date:  2016-11-11       Impact factor: 3.162

6.  Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins.

Authors:  Catherine A Kemme; Rolando Marquez; Ross H Luu; Junji Iwahara
Journal:  Nucleic Acids Res       Date:  2017-07-27       Impact factor: 16.971

Review 7.  Considering Abundance, Affinity, and Binding Site Availability in the NF-κB Target Selection Puzzle.

Authors:  Ruth Brignall; Amy T Moody; Shibin Mathew; Suzanne Gaudet
Journal:  Front Immunol       Date:  2019-03-29       Impact factor: 7.561

8.  Enhancement of gene expression noise from transcription factor binding to genomic decoy sites.

Authors:  Supravat Dey; Mohammad Soltani; Abhyudai Singh
Journal:  Sci Rep       Date:  2020-06-04       Impact factor: 4.379

9.  Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity.

Authors:  Xinyi Wan; Filipe Pinto; Luyang Yu; Baojun Wang
Journal:  Nat Commun       Date:  2020-11-24       Impact factor: 14.919

Review 10.  Zinc Finger Readers of Methylated DNA.

Authors:  Nicholas O Hudson; Bethany A Buck-Koehntop
Journal:  Molecules       Date:  2018-10-07       Impact factor: 4.411
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