ArticleGenome research2009
A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 167 citations in OpenAlex.
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- Measuring Interactions Between Proteins and Small Molecules or Nucleic Acids.Current protocols · 2024Review
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- Development of multifunctional synthetic nucleosomes to interrogate chromatin-mediated protein interactions.Science advances · 2023Article
- Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications.ACS chemical biology · 2023Review
- The emerging role of mass spectrometry-based proteomics in drug discovery.Nature reviews. Drug discovery · 2022Review
- Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization.International journal of molecular sciences · 2022Review
- Genetic Diversity of Transcription Factor Genes inFrontiers in plant science · 2022Article
- Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era.Journal of proteome research · 2021Review
- Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia.Trends in immunology · 2021Review
- Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene.Cell reports · 2021Article
- Deciphering the regulatory genome ofeLife · 2020Article
- Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer.Clinical & experimental metastasis · 2020Article
- Mass Spectrometry to Study Chromatin Compaction.Biology · 2020Review
- ChromID identifies the protein interactome at chromatin marks.Nature biotechnology · 2020Article
- Quantitative Proteomics Identifies TCF1 as a Negative Regulator of Foxp3 Expression in Conventional T Cells.iScience · 2020Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the underlying logic that governs the networks of gene expression in higher eukaryotes is an important task in the post-genome era. Sequence-specific transcription factors (TFs) that can read the genetic regulatory information and proteins that interpret the information provided by CpG methylation are crucial components of the system that controls the transcription of protein-coding genes by RNA polymerase II. We have previously described Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for the quantitative comparison of proteomes and the determination of protein-protein interactions. Here, we report a generic and scalable strategy to uncover such DNA protein interactions by SILAC that uses a fast and simple one-step affinity capture of TFs from crude nuclear extracts. Employing mutated or nonmethylated control oligonucleotides, specific TFs binding to their wild-type or methyl-CpG bait are distinguished from the vast excess of copurifying background proteins by their peptide isotope ratios that are determined by mass spectrometry. Our proof of principle screen identifies several proteins that have not been previously reported to be present on the fully methylated CpG island upstream of the human metastasis associated 1 family, member 2 gene promoter. The approach is robust, sensitive, and specific and offers the potential for high-throughput determination of TF binding profiles.
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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.