ArticleNucleic acids research2011
Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
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- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames.G3 (Bethesda, Md.) · 2025Article
- In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli.Communications biology · 2024Article
- Deletion of the Candida albicans TLO gene family using CRISPR-Cas9 mutagenesis allows characterisation of functional differences in α-, β- and γ- TLO gene function.PLoS genetics · 2023Article
- Changes in adenoviral chromatin organization precede early gene activation upon infection.The EMBO journal · 2023Article
- DNA-bridging by an archaeal histone variant via a unique tetramerisation interface.Communications biology · 2023Article
- Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development.Genes & development · 2023Article
- In situ tools for chromatin structural epigenomics.Protein science : a publication of the Protein Society · 2022Article
- CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells.Genome biology · 2022Article
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- The native cistrome and sequence motif families of the maize ear.PLoS genetics · 2021Article
- Repression of a large number of genes requires interplay between homologous recombination and HIRA.Nucleic acids research · 2021Article
- Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells.Nucleic acids research · 2020Article
- Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor.Molecular cell · 2020Article
- Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana.Genome biology · 2020Article
- Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.Nature structural & molecular biology · 2020Review
- Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag.Plant methods · 2020Article
- Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.Nucleic acids research · 2019Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray and next-generation sequencing techniques which allow whole genome analysis of chromatin structure and sequence-specific protein binding are revolutionizing our view of chromosome architecture and function. However, many current methods in this field rely on biochemical purification of highly specific fractions of DNA prepared from chromatin digested with either micrococcal nuclease or DNaseI and are restricted in the parameters they can measure. Here, we show that a broad size-range of genomic DNA species, produced by partial micrococcal nuclease digestion of chromatin, can be sequenced using paired-end mode next-generation technology. The paired sequence reads, rather than DNA molecules, can then be size-selected and mapped as particle classes to the target genome. Using budding yeast as a model, we show that this approach reveals position and structural information for a spectrum of nuclease resistant complexes ranging from transcription factor-bound DNA elements up to mono- and poly-nucleosomes. We illustrate the utility of this approach in visualizing the MNase digestion landscape of protein-coding gene transcriptional start sites, and demonstrate a comparative analysis which probes the function of the chromatin-remodelling transcription factor Cbf1p.
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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.