ArticleNucleic acids research2008
Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Foxi3 transcription factor activity is mediated by a C-terminal transactivation domain and regulated by the Protein Phosphatase 2A (PP2A) complex.Scientific reports · 2018Article
- Foxi transcription factors promote pharyngeal arch development by regulating formation of FGF signaling centers.Developmental biology · 2014Article
- Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data.BMC systems biology · 2013Article
- Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.PloS one · 2013Article
- Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development.BMC genomics · 2012Article
- Systematic characterization of protein-DNA interactions.Cellular and molecular life sciences : CMLS · 2011Review
- Lysine120 interactions with p53 response elements can allosterically direct p53 organization.PLoS computational biology · 2010Article
- Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.PLoS computational biology · 2009Article
- Functional analysis of transcription factors in Arabidopsis.Plant & cell physiology · 2009Review
- Article
- Characterization of genome-wide p53-binding sites upon stress response.Nucleic acids research · 2008Article
- Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios.Journal of molecular recognition : JMRArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
Abstract
Knowledge of all binding sites for transcriptional activators and repressors is essential for computationally aided identification of transcriptional networks. The techniques developed for defining the binding sites of transcription factors tend to be cumbersome and not adaptable to high throughput. We refined a versatile yeast strategy to rapidly and efficiently identify genomic targets of DNA-binding proteins. Yeast expressing a transcription factor is mated to yeast containing a library of genomic fragments cloned upstream of the reporter gene URA3. DNA fragments with target-binding sites are identified by growth of yeast clones in media lacking uracil. The experimental approach was validated with the tumor suppressor protein p53 and the forkhead protein FoxI1 using genomic libraries for zebrafish and mouse generated by shotgun cloning of short genomic fragments. Computational analysis of the genomic fragments recapitulated the published consensus-binding site for each protein. Identified fragments were mapped to identify the genomic context of each binding site. Our yeast screening strategy, combined with bioinformatics approaches, will allow both detailed and high-throughput characterization of transcription factors, scalable to the analysis of all putative DNA-binding proteins.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.