ArticleGenome biology2023
The CUT&RUN suspect list of problematic regions of the genome.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- PRDM9-mediated meiotic hotspot specification is constrained in humans despite extensive sequence diversity.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- CUT&RUN as a Powerful Tool for Chromatin Profiling: A Focus on Neuropsychiatric Disorders.Biological psychiatry · 2026Review
- Motif-Cluster: Motif driven prioritization of transcription factor binding clusters.PLoS computational biology · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- Article
- DNA Methyltransferase Inhibition Prevents Platinum-Induced Ovarian Cancer Stem Cell Enrichment.Cancer research communications · 2026Article
- Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN.STAR protocols · 2026Article
- Leukemia risk factor ARID5B coordinates HDAC-mediated transcriptional repression.Nucleic acids research · 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
- AID and TET2 cooperate to demethylate Irf4 for plasma cell fate in germinal center B cells.The Journal of experimental medicine · 2026Article
- Unstructured transcription factor interactions enable emergent specificity.Science (New York, N.Y.) · 2026Article
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- COUP-TFII regulates hemoglobin switching by activating the BCL11A-XL repressor LIN28B and directly binding δ and β globin promoters in fetalHaematologica · 2026Article
- Disruption of the SAGA CORE triggers collateral degradation of KAT2A.Nature communications · 2026Article
- Multiomic screening platform uncovers the impact of histone mutations on chromatin and cell fate.bioRxiv : the preprint server for biology · 2026Article
- Foxn3 is part of a transcriptional network that regulates primary cilia in the developing retina.Development (Cambridge, England) · 2026Article
- Mechanistic dissection of GRHL2 and PR transcriptional co-regulation in breast cells.PLoS genetics · 2026Article
- Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.Bioinformatics (Oxford, England) · 2026Article
- CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination.Nucleic acids research · 2026Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: these lists contain regions of high and unstructured signal, regardless of cell type or protein target, indicating that these are false positives. While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions.
resultsWe compile suspect lists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls. Using published CUT&RUN data from our and other labs, we show that the CUT&RUN suspect regions can persist even when peak calling is performed with SEACR or MACS2 against a negative control and after ENCODE blacklist removal. Moreover, we experimentally validate the CUT&RUN suspect lists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture more than 80% of the peaks identified.
conclusionsWe propose that removing these problematic regions can substantially improve peak calling in CUT&RUN experiments, resulting in more reliable datasets.
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