Nucleosome positioning in yeasts: methods, maps, and mechanisms

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Chromosoma

• Publication date

  2015-06-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1007/s00412-014-0501-xPMID 25529773
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Comparative analysis of methods for genome-wide nucleosome cartography

  2015cited by this paper
• Two independent transcription initiation codes overlap on vertebrate core promoters

  2014cited by this paper
• A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

  2014cited by this paper
• Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

  2014influential reference
• A comparative evaluation on prediction methods of nucleosome positioning

  2014cited by this paper
• Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

  2014cited by this paper
• Chromatin as dynamic 10-nm fibers

  2014influential reference
• The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin

  2014cited by this paper
• Genome‐Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High‐Resolution Histone ChIP, and NCAM

  2014influential reference
• Fuzziness and noise in nucleosomal architecture

  2014cited by this paper
• Ubiquitous nucleosome crowding in the yeast genome

  2014cited by this paper
• Mechanisms underlying nucleosome positioning in vivo.

  2014cited by this paper
• RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast

  2014cited by this paper
• A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme

  2013cited by this paper
• DNA looping facilitates targeting of a chromatin remodeling enzyme.

  2013cited by this paper
• Analysis of chromatin organization by deep sequencing technologies.

  2013cited by this paper
• Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

  2013cited by this paper
• A Detailed Protocol for Formaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE)

  2013cited by this paper
• Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

  2013influential reference
• Nucleosome remodeling and epigenetics.

  2013cited by this paper
• Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

  2013cited by this paper
• ISWI and CHD chromatin remodelers bind to promoters but act in gene bodies

  2013cited by this paper
• SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes.

  2013cited by this paper
• Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.

  2013cited by this paper
• Nucleosome-free region dominates histone acetylation in targeting SWR1 to promoters for H2A.Z replacement.

  2013cited by this paper
• Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

  2013cited by this paper
• Toward a unified physical model of nucleosome patterns flanking transcription start sites

  2013cited by this paper
• A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

  2013influential reference
• Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae.

  2013influential reference
• NucleoFinder: a statistical approach for the detection of nucleosome positions

  2013cited by this paper
• Determinants of nucleosome positioning

  2013cited by this paper
• Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast

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• Genome-wide Mapping

  2013influential reference
• DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

  2013cited by this paper
• ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

  2013cited by this paper
• Specification of DNA replication origins and genomic base composition in fission yeasts.

  2013influential reference
• Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing

  2012cited by this paper
• In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae

  2012cited by this paper
• Genome-wide mapping of nucleosomes in yeast using paired-end sequencing.

  2012influential reference
• Hrp3 controls nucleosome positioning to suppress non‐coding transcription in eu‐ and heterochromatin

  2012cited by this paper
• Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

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• A base pair resolution map of nucleosome positions in yeast

  2012influential reference
• Computational analysis of nucleosome positioning.

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• Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

  2012influential reference
• Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

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• Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

  2012influential reference
• Genome-wide nucleosome specificity and directionality of chromatin remodelers.

  2012influential reference
• Linker histone subtypes differ in their effect on nucleosomal spacing in vivo.

  2012influential reference
• CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe

  2012cited by this paper
• Nucleosome positioning: bringing order to the eukaryotic genome.

  2012cited by this paper
• A chemical approach to mapping nucleosomes at base pair resolution in yeast.

  2012influential reference
• Chromatin architectures at fission yeast transcriptional promoters and replication origins

  2012influential reference
• A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern.

  2012influential reference
• Genome-wide mapping of nucleosome positions in yeast using high-resolution MNase ChIP-Seq.

  2012cited by this paper
• Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

  2012cited by this paper
• The Linker Histone Plays a Dual Role during Gametogenesis in Saccharomyces cerevisiae

  2012cited by this paper
• NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data

  2012cited by this paper
• Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1.

  2012cited by this paper
• Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution.

  2012cited by this paper
• Genome-wide in vitro reconstitution of yeast chromatin with in vivo-like nucleosome positioning.

  2012cited by this paper
• Genome-wide identification and characterization of replication origins by deep sequencing

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• In vitro reconstitution of in vivo-like nucleosome positioning on yeast DNA.

  2012cited by this paper
• Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

  2012cited by this paper
• Genomic approaches for determining nucleosome occupancy in yeast.

  2012cited by this paper
• Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs

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• Perfect and imperfect nucleosome positioning in yeast.

  2012influential reference
• Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

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• A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

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• The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4

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• Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes

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• Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters

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• Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

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• The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes

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• Genome-wide structure and organization of eukaryotic pre-initiation complexes

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• Structure and mechanism of the chromatin remodelling factor ISW1a

  2011cited by this paper
• Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.

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• Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.

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• Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes

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• Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output

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• Determinants and dynamics of genome accessibility

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• High-resolution genome-wide mapping of the primary structure of chromatin.

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• A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

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• The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere

  2011influential reference
• Stable and dynamic nucleosome states during a meiotic developmental process.

  2011influential reference
• Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.

  2011influential reference
• Epigenome characterization at single base-pair resolution

  2011influential reference
• Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen

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• Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity.

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• nucleR: a package for non-parametric nucleosome positioning

  2011cited by this paper
• Determinants of nucleosome organization in primary human cells

  2011cited by this paper
• Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast

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• Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns

  2011cited by this paper
• Nucleosome Positioning in Saccharomyces cerevisiae

  2011cited by this paper
• A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding.

  2010cited by this paper
• The Role of Nucleosome Positioning in the Evolution of Gene Regulation

  2010influential reference
• Nucleosome positioning: how is it established, and why does it matter?

  2010cited by this paper
• High-resolution nucleosome mapping reveals transcription-dependent promoter packaging.

  2010influential reference
• Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae

  2010influential reference
• Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

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• Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure

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  2025cites this paper
• Genome organization across scales: mechanistic insights from in vitro reconstitution studies

  2024cites this paper
• An integrated machine-learning model to predict nucleosome architecture

  2024cites this paper
• In silico design of DNA sequences for in vivo nucleosome positioning

  2023cites this paper
• GC content strongly influences the role of poly(dA) in the intrinsic nucleosome positioning in Saccharomyces cerevisiae

  2022cites this paper
• Dynamic nucleosome landscape elicits a noncanonical GATA2 pioneer model

  2022cites this paper
• Mammalian Micro-C-XL.

  2022cites this paper
• Peculiarities of Plasmodium falciparum Gene Regulation and Chromatin Structure

  2021cites this paper
• Mapping of Nonhomologous End Joining-Mediated Integration Facilitates Genome-Scale Trackable Mutagenesis in Yarrowia lipolytica.

  2021cites this paper
• The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo

  2021cites this paper
• The Active Rather than Intrinsic Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts

  2021cites this paper
• Beads on a string—nucleosome array arrangements and folding of the chromatin fiber

  2020cites this paper
• Effective dynamics of nucleosome configurations at the yeast PHO5 promoter

  2020cites this paper
• Linker DNA Length is a Key to Tri-nucleosome Folding.

  2020cites this paper
• Limited expression of non-integrating CpG-free plasmid is associated with increased nucleosome enrichment

  2020cites this paper
• Genome information processing by the INO80 chromatin remodeler positions nucleosomes

  2020cites this paper
• Slow motions in A·T rich DNA sequence

  2020cites this paper
• A dynamic view of DNA structure within the nucleosome: biological implications.

  2020cites this paper
• Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae.

  2020cites this paper
• Chromatin Immunoprecipitation

  2020influential citation
• [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature].

  2020cites this paper
• Nucleosome sliding mechanism based on the potential energy of sequence.

  2020cites this paper
• Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

  2019cites this paper
• RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast.

  2019cites this paper
• Nucleosome positioning and spacing: from genome-wide maps to single arrays.

  2019cites this paper
• ZCMM: A Novel Method Using Z-Curve Theory- Based and Position Weight Matrix for Predicting Nucleosome Positioning

  2019cites this paper
• Epigenome Regulation by Dynamic Nucleosome Unwrapping.

  2019cites this paper
• Role of general regulatory factors in the control of gene expression and transcription fidelity

  2019cites this paper
• Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos

  2019cites this paper
• Title : 1 Chemical map – based prediction of nucleosome positioning using the 2 Bioconductor package nuCpos

  2019cites this paper
• Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation

  2019cites this paper
• Sequence-directed action of RSC remodeler and pioneer factors positions +1 nucleosome to facilitate transcription

  2018cites this paper
• General Regulatory Factors control the fidelity of transcription by restricting non-coding and ectopic initiation

  2018cites this paper
• Genome-wide Rules of Nucleosome Phasing in Drosophila.

  2018cites this paper
• Characterization of the Nucleosome Landscape by Micrococcal Nuclease-Sequencing (MNase-seq).

  2018cites this paper
• ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation

  2018cites this paper
• Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription.

  2018cites this paper
• Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler.

  2017cites this paper
• Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy.

  2017cites this paper
• Dissection of nucleosome positioning mechanisms by genome-wide in vitro reconstitution

  2017influential citation
• Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

  2016cites this paper
• A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions

  2016cites this paper
• Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

  2016cites this paper
• Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin

  2016cites this paper
• Genome-wide analysis of phased nucleosomal arrays reveals the functional characteristic of the nucleosome remodeler ACF

  2016cites this paper
• Genome-wide rules of nucleosome phasing

  2016influential citation
• A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

  2015cites this paper
• Defining the chromatin structure of the human genome using size-selected nucleosome mapping

  2015cites this paper
• The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

  2015influential citation
• Distinct nucleosome distribution patterns in two structurally and functionally differentiated nuclei of a unicellular eukaryote

  2015cites this paper
• Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast.

  2015cites this paper
• Dynamic regulation of transcription factors by nucleosome remodeling

  2015influential citation
• Nucleosome positioning: resources and tools online

  2015cites this paper