ArticleGenome research2007
Calling cards for DNA-binding proteins.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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
27 citing papers in PubMed, 37 citations in OpenAlex.
- Scalable transcription factor mapping uncovers the regulatory dynamics of natural and synthetic transcription factors in human T cell states.bioRxiv : the preprint server for biology · 2025Article
- Genomic Mosaicism of the Brain: Origin, Impact, and Utility.Neuroscience bulletin · 2024Review
- Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data.Bioinformatics (Oxford, England) · 2024Article
- Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues.Current protocols · 2023Article
- Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.Nucleic acids research · 2023Article
- Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues.bioRxiv : the preprint server for biology · 2023Article
- NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration.Bioinformatics (Oxford, England) · 2023Article
- Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.NAR genomics and bioinformatics · 2022Article
- The qBED track: a novel genome browser visualization for point processes.Bioinformatics (Oxford, England) · 2021Article
- Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ).Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays.Nucleic acids research · 2020Article
- Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes.Genetics · 2020Article
- Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.Annual review of cell and developmental biology · 2019Review
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- O Cdc7 kinase where art thou?Current genetics · 2018Article
- Localization of Cdc7 Protein Kinase During DNA Replication inG3 (Bethesda, Md.) · 2017Article
- An optimized, broadly applicable piggyBac transposon induction system.Nucleic acids research · 2017Article
- Mapping yeast transcriptional networks.Genetics · 2013Review
- RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay.RNA (New York, N.Y.) · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Identifying genomic targets of transcription factors is fundamental for understanding transcriptional regulatory networks. Current technology enables identification of all targets of a single transcription factor, but there is no realistic way to achieve the converse: identification of all proteins that bind to a promoter of interest. We have developed a method that promises to fill this void. It employs the yeast retrotransposon Ty5, whose integrase interacts with the Sir4 protein. A DNA-binding protein fused to Sir4 directs insertion of Ty5 into the genome near where it binds; the Ty5 becomes a "calling card" the DNA-binding protein leaves behind in the genome. We constructed customized calling cards for seven transcription factors of yeast by including in each Ty5 a unique DNA sequence that serves as a "molecular bar code." Ty5 transposition was induced in a population of yeast cells, each expressing a different transcription factor-Sir4 fusion and its matched, bar-coded Ty5, and the calling cards deposited into selected regions of the genome were identified, revealing the transcription factors that visited that region of the genome. In each region we analyzed, we found calling cards for only the proteins known to bind there: In the GAL1-10 promoter we found only calling cards for Gal4; in the HIS4 promoter we found only Gcn4 calling cards; in the PHO5 promoter we found only Pho4 and Pho2 calling cards. We discuss how Ty5 calling cards might be implemented for mapping all targets of all transcription factors in a single experiment.
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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.