ArticleNature communications2026
PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility.bioRxiv : the preprint server for biology · 2026Article
- Response to the commentary by Melidis et al. on "Untargeted CUT&Tag reads are enriched at accessible chromatin and restrict identification of potential G4-forming sequences in G4-targeted CUT&Tag experiments".Nucleic acids research · 2025Article
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8 authors.
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Abstract
Accurate epigenomic profiling is essential for understanding chromatin and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) enables efficient epigenomic profiling for low-input and single-cell samples and is increasingly adopted in genomics research. However, CUT&Tag's usage of Tn5 transposase introduces bias toward open chromatin that distorts genome-wide signal patterns and confounds downstream analysis, especially in sparse single-cell data. We show that open-chromatin bias extensively exists in published CUT&Tag data, including those generated with optimized high-salt protocols. To address this issue, we present PATTY (Propensity Analyzer for Tn5 Transposase Yielded bias), a computational method that corrects open-chromatin bias in CUT&Tag by leveraging accompanying ATAC-seq using machine learning. PATTY enables accurate and robust signal detection for both active and repressive histone modifications, including H3K27ac, H3K27me3, and H3K9me3. In single-cell CUT&Tag analyses, PATTY bias correction improves cell clustering accuracy. Beyond CUT&Tag, PATTY establishes a generalizable framework for bias correction in Tn5-based genomic assays.
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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.