ArticleDevelopment (Cambridge, England)2022
A new CUT&RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets.
Article in Development (Cambridge, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 29 citations in OpenAlex.
- CUT&ID for simultaneous profiling of protein-DNA and protein-protein interactions.Nucleic acids research · 2026Article
- HKDC1-mediated polyamine rewiring drives lenvatinib resistance and immune escape in hepatocellular carcinoma.Clinical and molecular hepatology · 2026Article
- Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN.STAR protocols · 2026Article
- Differential Wnt/β-catenin signaling via TCF7L2/LEF1 binding specificity shapes cellular and tumor phenotypes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atg8 orchestrates stress-responsive chromatin programs across immunity and metabolism.bioRxiv : the preprint server for biology · 2026Article
- COUP-TFII regulates hemoglobin switching by activating the BCL11A-XL repressor LIN28B and directly binding δ and β globin promoters in fetalHaematologica · 2026Article
- Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells.PLoS genetics · 2026Article
- Wnt signaling activation induces CTCF binding and loop formation atGenome research · 2025Article
- DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution.Nature communications · 2025Article
- Multi-omics based and AI-driven drug repositioning for epigenetic therapy in female malignancies.Journal of translational medicine · 2025Review
- The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- TGFβ signaling sensitizes MEKi-resistant human melanoma to targeted therapy-induced apoptosis.Cell death & disease · 2024Article
- The scaffolding function of LSD1 controls DNA methylation in mouse ESCs.Nature communications · 2024Article
- Exhaustive identification of genome-wide binding events of transcriptional regulators.Nucleic acids research · 2024Article
- The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping.Briefings in bioinformatics · 2024Article
- The CUT&RUN suspect list of problematic regions of the genome.Genome biology · 2023Article
- β-Catenin Drives Butyrophilin-like Molecule Loss and γδ T-cell Exclusion in Colon Cancer.Cancer immunology research · 2023Article
- Stress-sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis.Molecular systems biology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Upon WNT/β-catenin pathway activation, stabilized β-catenin travels to the nucleus where it associates with the TCF/LEF transcription factors, constitutively bound to genomic Wnt-responsive elements (WREs), to activate target gene transcription. Discovering the binding profile of β-catenin is therefore required to unambiguously assign direct targets of WNT signaling. Cleavage under targets and release using nuclease (CUT&RUN) has emerged as prime technique for mapping the binding profile of DNA-interacting proteins. Here, we present a modified version of CUT&RUN, named LoV-U (low volume and urea), that enables the robust and reproducible generation of β-catenin binding profiles, uncovering direct WNT/β-catenin target genes in human cells, as well as in cells isolated from developing mouse tissues. CUT&RUN-LoV-U outperforms original CUT&RUN when targeting co-factors that do not bind the DNA, can profile all classes of chromatin regulators and is well suited for simultaneous processing of several samples. We believe that the application of our protocol will allow the detection of the complex system of tissue-specific WNT/β-catenin target genes, together with other non-DNA-binding transcriptional regulators that act downstream of ontogenetically fundamental signaling cascades.
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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.