ArticleGenome biology2017
NicE-seq: high resolution open chromatin profiling.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Methylation Mesa define functional regulatory elements for targeted gene activation.Nature communications · 2026Article
- Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape.bioRxiv : the preprint server for biology · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Normozoospermic infertile men possess subpopulations of sperm varying in DNA accessibility, relating to differing reproductive outcomes.Human reproduction (Oxford, England) · 2025Article
- Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing.Nucleic acids research · 2025Article
- NUP37 promotes the proliferation and invasion of glioma cells through DNMT1-mediated methylation.Cell death discovery · 2024Article
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology.International journal of molecular sciences · 2023Review
- Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.Nature genetics · 2022Article
- NicE-C efficiently reveals open chromatin-associated chromosome interactions at high resolution.Genome research · 2022Article
- Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq.Methods in molecular biology (Clifton, N.J.) · 2022Article
- One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics.Epigenetics & chromatin · 2021Article
- Review
- Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seq captures and reveals open chromatin sites (OCSs) and transcription factor occupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden. OCSs correlate with RNA polymerase II occupancy and active chromatin marks, while displaying a contrasting pattern to CpG methylation. Decitabine-mediated hypomethylation of HCT116 displays higher numbers of OCSs.
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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.