ArticleNucleic acids research2019
NextPBM: a platform to study cell-specific transcription factor binding and cooperativity.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 49 citations in OpenAlex.
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- Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.bioRxiv : the preprint server for biology · 2026Article
- Combinatorial transcription factor interactions drive modular gene regulatory networks.bioRxiv : the preprint server for biology · 2026Article
- Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals.bioRxiv : the preprint server for biology · 2026Article
- USP20, a Super-enhancer Regulated Gene, Promotes Acute Myeloid Leukemia Progression through CTNNB1 Deubiquitination.International journal of biological sciences · 2026Article
- Core transcriptional regulatory circuitry molecule ZNF217 promotes AML cell proliferation by up-regulating MYB.International journal of biological sciences · 2025Article
- Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming.PLoS biology · 2024Article
- Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation.Nucleic acids research · 2024Article
- Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation.bioRxiv : the preprint server for biology · 2024Article
- Utilizing nuclear extracts to characterize protein: DNA interactions at the single molecule level.Methods in enzymology · 2024Article
- DNA selection by the master transcription factor PU.1.Cell reports · 2023Article
- Widespread perturbation of ETS factor binding sites in cancer.Nature communications · 2023Article
- Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.Nature communications · 2023Article
- Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia.iScience · 2022Article
- Super-enhancer profiling identifies novel critical and targetable cancer survival gene LYL1 in pediatric acute myeloid leukemia.Journal of experimental & clinical cancer research : CR · 2022Article
- KHSRP combines transcriptional and posttranscriptional mechanisms to regulate monocytic differentiation.Blood science (Baltimore, Md.) · 2022Article
- Autophagy enhanced by curcumin ameliorates inflammation in atherogenesisActa pharmaceutica Sinica. B · 2022Article
- Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery.Nature communications · 2022Article
- CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.Cell genomics · 2022Article
- The Non-continuum Nature of Eukaryotic Transcriptional Regulation.Advances in experimental medicine and biology · 2022Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput (HT) in vitro methods for measuring protein-DNA binding have become invaluable for characterizing transcription factor (TF) complexes and modeling gene regulation. However, current methods do not utilize endogenous proteins and, therefore, do not quantify the impact of cell-specific post-translational modifications (PTMs) and cooperative cofactors. We introduce the HT nextPBM (nuclear extract protein-binding microarray) approach to study DNA binding of native cellular TFs that accounts for PTMs and cell-specific cofactors. We integrate immune-depletion and phosphatase treatment steps into our nextPBM pipeline to characterize the impact of cofactors and phosphorylation on TF binding. We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative cofactors. We describe how nextPBMs, and our accompanying computational framework, can be used to discover cell-specific cofactors, screen for synthetic cooperative DNA elements, and characterize TF cooperativity.
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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.