ArticleMolecular systems biology2013
A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks.
Article in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq.Nature genetics · 2025Article
- Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors.Nature communications · 2023Article
- Enhanced Yeast One-Hybrid Assays to Study Protein-DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle.iScience · 2022Article
- Article
- Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays.Genome research · 2019Article
- Microfluidic epigenomic mapping technologies for precision medicine.Lab on a chip · 2019Review
- High-Throughput Yeast One-Hybrid Screens Using a Cell Surface gLUC Reporter.Current protocols in plant biology · 2019Article
- Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences.Journal of visualized experiments : JoVE · 2019Article
- Mitotic chromosome binding predicts transcription factor properties in interphase.Nature communications · 2019Article
- REDfly: the transcriptional regulatory element database for Drosophila.Nucleic acids research · 2019Article
- ZNF445 is a primary regulator of genomic imprinting.Genes & development · 2019Article
- Automated microfluidic droplet sampling with integrated, mix-and-read immunoassays to resolve endocrine tissue secretion dynamics.Lab on a chip · 2018Article
- Novel cell surface luciferase reporter for high-throughput yeast one-hybrid screens.Nucleic acids research · 2017Article
- RIP4 inhibits STAT3 signaling to sustain lung adenocarcinoma differentiation.Cell death and differentiation · 2017Article
- A mouse tissue transcription factor atlas.Nature communications · 2017Article
- Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.The Journal of biological chemistry · 2016Article
- Microfluidics: reframing biological enquiry.Nature reviews. Molecular cell biology · 2015Review
- Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing.Nature communications · 2015Article
- Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression by identifying their trans-regulatory inputs. Here, we present the generation of a mouse-specific transcription factor (TF) open-reading frame clone library and its implementation in yeast one-hybrid assays to enable large-scale protein-DNA interaction detection with mouse regulatory elements. Once specific interactions are identified, we then use a microfluidics-based method to validate and precisely map them within the respective DNA sequences. Using well-described regulatory elements as well as orphan enhancers, we show that this cross-platform pipeline characterizes known and uncovers many novel TF-DNA interactions. In addition, we provide evidence that several of these novel interactions are relevant in vivo and aid in elucidating the regulatory architecture of enhancers.
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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.