Changing chromatin fiber conformation by nucleosome repositioning

scientific article

Changing chromatin fiber conformation by nucleosome repositioning is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.BPJ.2014.09.026
P932PMC publication ID4223204
P698PubMed publication ID25418099

P50authorKarsten RippeQ38800586
Gero WedemannQ41548222
P2093author name stringOliver Müller
Robert Schöpflin
Nick Kepper
Ramona Ettig
P2860cites workCrystal structure of the nucleosome core particle at 2.8 A resolutionQ22122355
EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structureQ24542512
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioningQ24650871
Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatinQ24652372
Toward convergence of experimental studies and theoretical modeling of the chromatin fiberQ26852454
H1 histones: current perspectives and challengesQ27023358
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolutionQ27639217
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationQ27860944
Genome-wide nucleosome positioning during embryonic stem cell developmentQ28277658
Cryo-electron microscopy of vitrified specimensQ28288841
Dynamic regulation of nucleosome positioning in the human genomeQ29615046
The biology of chromatin remodeling complexesQ29620581
Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situQ30485080
Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structureQ30512823
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivoQ33659597
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sitesQ33680648
Dynamics of nucleosome remodelling by individual ACF complexesQ33716234
Determinants of nucleosome organization in primary human cellsQ34027018
Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nucleiQ34039312
Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitroQ34090023
Living without 30nm chromatin fibersQ34142094
Mechanisms of ATP-dependent nucleosome slidingQ34165927
Mechanisms for ATP-dependent chromatin remodelling: the means to the endQ34170937
Controlling the double helixQ34172152
Computer simulation of the 30-nanometer chromatin fiber.Q34177968
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genomeQ34186316
Nucleosome arrays reveal the two-start organization of the chromatin fiberQ34371762
Rapid spontaneous accessibility of nucleosomal DNA.Q34373646
Genome-scale identification of nucleosome positions in S. cerevisiaeQ34427114
X-ray structure of a tetranucleosome and its implications for the chromatin fibreQ34431881
Controls of nucleosome positioning in the human genome.Q34481868
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.Q34613479
ATP-dependent chromatin remodeling: genetics, genomics and mechanismsQ34627244
Chromatin remodelling in mammalian cells by ISWI-type complexes--where, when and why?Q34631370
The RSC chromatin remodelling ATPase translocates DNA with high force and small step sizeQ35048885
Keeping fingers crossed: heterochromatin spreading through interdigitation of nucleosome arraysQ35749599
Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extractsQ35962959
Internucleosomal interactions mediated by histone tails allow distant communication in chromatinQ36016884
Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanismQ36058611
The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbonQ36234105
Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat lengthQ36234129
Organization of interphase chromatinQ36346077
A chromatin folding model that incorporates linker variability generates fibers resembling the native structuresQ36567800
Higher-order structures of chromatin: the elusive 30 nm fiberQ36744470
ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit stepsQ36825396
Nucleosome positioning and gene regulation: advances through genomicsQ36883122
Insights into chromatin fibre structure by in vitro and in silico single-molecule stretching experimentsQ36933057
Hidden Markov analysis of nucleosome unwrapping under forceQ37263583
Chromatin structure: does the 30-nm fibre exist in vivo?Q37719900
Electrostatics at the nanoscaleQ37842183
The dynamics of the nucleosome: thermal effects, external forces and ATP.Q37910985
Modelling chromatin structure and dynamics: status and prospectsQ37981348
Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.Q38699004
Histone depletion facilitates chromatin loops on the kilobasepair scale.Q38973166
Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagramsQ39888329
Nucleosome shape dictates chromatin fiber structureQ40005967
A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytesQ40224716
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomeQ41336121
Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal unitsQ41608597
Affinity, stoichiometry and cooperativity of heterochromatin protein 1 (HP1) binding to nucleosomal arraysQ41617674
High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genomeQ41777561
Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformationQ41832209
A map of nucleosome positions in yeast at base-pair resolutionQ41968064
Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequenceQ42132377
The effect of internucleosomal interaction on folding of the chromatin fiberQ42943386
Force spectroscopy of chromatin fibers: extracting energetics and structural information from Monte Carlo simulationsQ43838369
Modeling nucleosome position distributions from experimental nucleosome positioning mapsQ47869903
DNA-DNA interactions in tight supercoils are described by a small effective charge density.Q51613997
Replica Monte Carlo simulation of spin glasses.Q55032678
Interdigitated Solenoid Model for Compact Chromatin Fibers†Q58944557
Polymer reptation and nucleosome repositioningQ73818559
Nucleosome interactions in chromatin: fiber stiffening and hairpin formationQ80481143
NAP1 modulates binding of linker histone H1 to chromatin and induces an extended chromatin fiber conformationQ81073936
Nucleosome positioning and nucleosome stacking: two faces of the same coinQ83299001
Structure of the 300A chromatin filament: X-ray diffraction from oriented samplesQ93658325
P433issue9
P407language of work or nameEnglishQ1860
P304page(s)2141-2150
P577publication date2014-11-01
P1433published inBiophysical JournalQ2032955
P1476titleChanging chromatin fiber conformation by nucleosome repositioning
P478volume107

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cites work (P2860)
Q57136695A Guided Protocol for Array Based T2C: A High-Quality Selective High-Resolution High-Throughput Chromosome Interaction Capture
Q91187980Chromatin accessibility and the regulatory epigenome
Q92646479Nucleosome positions alone can be used to predict domains in yeast chromosomes
Q35768249The chromatin fiber: multiscale problems and approaches
Q30833339The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.

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