ArticleeLife2016
A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution.
Article in eLife, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Article
- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- Article
- Control of Inflammatory Response by Tissue Microenvironment.bioRxiv : the preprint server for biology · 2025Article
- Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer.Non-coding RNA · 2025Review
- Size-based expectation maximization for characterizing nucleosome positions and subtypes.Genome research · 2024Article
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes.bioRxiv : the preprint server for biology · 2023Article
- Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.International journal of molecular sciences · 2022Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Hi-CO: 3D genome structure analysis with nucleosome resolution.Nature protocols · 2021Article
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.Genome biology · 2020Article
- Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction.Plant cell reports · 2018Review
- Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.Epigenetics & chromatin · 2017Article
- Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation.Genes & development · 2017Article
- Article
- Understanding nucleosome dynamics and their links to gene expression and DNA replication.Nature reviews. Molecular cell biology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Understanding chromatin function requires knowing the precise location of nucleosomes. MNase-seq methods have been widely applied to characterize nucleosome organization in vivo, but generally lack the accuracy to determine the precise nucleosome positions. Here we develop a computational approach leveraging digestion variability to determine nucleosome positions at a base-pair resolution from MNase-seq data. We generate a variability template as a simple error model for how MNase digestion affects the mapping of individual nucleosomes. Applied to both yeast and human cells, this analysis reveals that alternatively positioned nucleosomes are prevalent and create significant heterogeneity in a cell population. We show that the periodic occurrences of dinucleotide sequences relative to nucleosome dyads can be directly determined from genome-wide nucleosome positions from MNase-seq. Alternatively positioned nucleosomes near transcription start sites likely represent different states of promoter nucleosomes during transcription initiation. Our method can be applied to map nucleosome positions in diverse organisms at base-pair resolution.
Indexed as
Identifiers
What OpenQuestion holds
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.