ArticleNucleic acids research2011
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- On the dependent recognition of some long zinc finger proteins.Nucleic acids research · 2023Article
- I-Block: a simple Escherichia coli-based assay for studying sequence-specific DNA binding of proteins.Nucleic acids research · 2020Article
- Adaptive Landscapes in the Age of Synthetic Biology.Molecular biology and evolution · 2019Review
- Mapping DNA sequence to transcription factor binding energy in vivo.PLoS computational biology · 2019Article
- Zinc-finger domains in metazoans: evolution gone wild.Genome biology · 2017Article
- Modeling protein-DNA binding via high-throughput in vitro technologies.Briefings in functional genomics · 2017Article
- Past Roadblocks and New Opportunities in Transcription Factor Network Mapping.Trends in genetics : TIG · 2016Review
- LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression.Nucleic acids research · 2016Article
- A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.Nucleic acids research · 2015Article
- Spec-seq: determining protein-DNA-binding specificity by sequencing.Briefings in functional genomics · 2015Review
- High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.Genetics · 2014Article
- An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.Nucleic acids research · 2014Article
- Modeling the specificity of protein-DNA interactions.Quantitative biology (Beijing, China) · 2013Article
- Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases.Nucleic acids research · 2013Article
- Engineered zinc-finger proteins can compensate genetic haploinsufficiency by transcriptional activation of the wild-type allele: application to Willams-Beuren syndrome and supravalvular aortic stenosis.Human gene therapy · 2012Article
- An optimized two-finger archive for ZFN-mediated gene targeting.Nature methods · 2012Article
- Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.Microbiology and molecular biology reviews : MMBR · 2012Review
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6 authors.
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Abstract
We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We can obtain even more accurate binding models using a modified version of B1H selection method with constrained variation (CV-B1H). However, achieving these improved models using CV-B1H data required the development of a new method of analysis--GRaMS (Growth Rate Modeling of Specificity)--that estimates bacterial growth rates as a function of the quality of the recognition sequence. We benchmark these different methods of motif discovery using Zif268, a well-characterized C(2)H(2) zinc-finger TF on both a 28 bp randomized library for the standard B1H method and on 6 bp randomized library for the CV-B1H method for which 45 different experimental conditions were tested: five time points and three different IPTG and 3-AT concentrations. We find that GRaMS analysis is robust to the different experimental parameters whereas other analysis methods give widely varying results depending on the conditions of the experiment. Finally, we demonstrate that the CV-B1H assay can be performed in liquid media, which produces recognition models that are similar in quality to sequences recovered from selection on solid media.
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