ArticleNature methods2014
Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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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.
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Who cites it
40 citing papers in PubMed, 61 citations in OpenAlex.
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- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.JCI insight · 2021Article
- Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion.Life science alliance · 2019Article
- Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals.Nature communications · 2019Article
- Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development.Nucleic acids research · 2018Article
- RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF.Nucleic acids research · 2018Article
- Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.Nature communications · 2018Article
- Epigenomics: Technologies and Applications.Circulation research · 2018Review
- Fine-Resolution Mapping of TF Binding and Chromatin Interactions.Cell reports · 2018Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis.NPJ genomic medicine · 2018Article
- Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.Bioinformatics (Oxford, England) · 2017Article
- Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data.National science review · 2016Article
- Genetic assimilation: a review of its potential proximate causes and evolutionary consequences.Annals of botany · 2016Review
- Mapping nucleosome positions using DNase-seq.Genome research · 2016Article
- Genomic footprinting.Nature methods · 2016Review
- Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay.Genome biology · 2016Article
- Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.Cell · 2016Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
It is currently not possible to resolve the genome-wide relationship of transcription factors (TFs) and nucleosomes at the level of individual chromatin templates despite rapidly increasing data on TF and nucleosome occupancy in the human genome. Here we describe DNase I-released fragment-length analysis of hypersensitivity (DNase-FLASH), an approach that directly couples mapping of TF occupancy, via quantification of DNA microfragments released from individual TF recognition sites in regulatory DNA, to the surrounding nucleosome architecture, via analysis of larger DNA fragments, in a single assay. DNase-FLASH enables coupling of individual TF footprints to nucleosome occupancy, identifying TFs that precisely demarcate the regulatory DNA-nucleosome interface.
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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.