4.8 Article

Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

The fork protection complex recruits FACT to reorganize nucleosomes during replication

Barbara Safaric et al.

Summary: Chromosome replication relies on the recruitment of the nucleosome reorganization activity of the histone chaperone FACT, with coordination from the middle and C-terminal domains of Spt16 and Pob3. The N-terminal region plays a critical role in recruitment by the fork protection complex subunit Tof1. These interactions are essential for robust replication in vitro.

NUCLEIC ACIDS RESEARCH (2022)

Article Biology

Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT

Anastasiia L. Sivkina et al.

Summary: Sivkina et al. characterized the interaction between S. cerevisiae histone chaperone FACT and the nucleosome core particle. They found that FACT adopts a more open geometry in the presence of Nhp6, and together they unfold nucleosomes. Nhp6 alters the structure of FACT and the properties of nucleosomes to support nucleosome unfolding.

COMMUNICATIONS BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Structure of a backtracked hexasomal intermediate of nucleosome transcription

Lucas Farnung et al.

Summary: During gene transcription, the presence of human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS facilitates efficient nucleosome passage by RNA polymerase II.

MOLECULAR CELL (2022)

Article Multidisciplinary Sciences

Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT

Haruhiko Ehara et al.

Summary: This study used cryo-electron microscopy to obtain structures of RNA polymerase II (RNAPII) passing through nucleosomes during gene transcription. The researchers also identified the roles of transcription elongation factors and histone chaperones in nucleosome disassembly and reassembly.

SCIENCE (2022)

Article Biochemistry & Molecular Biology

The lane-switch mechanism for nucleosome repositioning by DNA translocase

Fritz Nagae et al.

Summary: Translocases involved in eukaryotic DNA transcription, replication, and repair encounter nucleosomes formed by histone octamers wrapped around genomic DNA, triggering downstream repositioning of nucleosomes. This study identified a lane-switch mechanism for downstream repositioning, where wrapped DNA switches binding lanes after unwrapping, providing insights into transcription through nucleosomes and histone recycling.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study

Giovanni B. Brandani et al.

Summary: Nucleosomes, consisting of DNA wrapped around histone proteins, are fundamental units of Eukaryotic chromosomes that compact the genome and regulate gene expression. Molecular dynamics simulations have provided insights into the kinetics, structure, and influencing factors of nucleosome assembly. The study found that histones and DNA can form various non-canonical nucleosome conformations during the complex assembly process, which remains unclear in detail.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Rad54 Drives ATP Hydrolysis-Dependent DNA Sequence Alignment during Homologous Recombination

J. Brooks Crickard et al.

Article Biochemistry & Molecular Biology

The role of FACT in managing chromatin: disruption, assembly, or repair?

Tim Formosa et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Structural Insights into ceNAP1 Chaperoning Activity toward ceH2A-H2B

Yongrui Liu et al.

STRUCTURE (2019)

Review Biochemistry & Molecular Biology

Fuzziness in Protein Interactions-A Historical Perspective

Monika Fuxreiter

JOURNAL OF MOLECULAR BIOLOGY (2018)

Article Multidisciplinary Sciences

High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes

Alexander Gansen et al.

NATURE COMMUNICATIONS (2018)

Review Cell Biology

Understanding nucleosome dynamics and their links to gene expression and DNA replication

William K. M. Lai et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Review Cell Biology

Histone chaperone networks shaping chromatin function

Colin M. Hammond et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Biochemical Research Methods

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

Toru Niina et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly

Carmen Aguilar-Gurrieri et al.

EMBO JOURNAL (2016)

Review Chemistry, Multidisciplinary

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

Shoji Takada et al.

ACCOUNTS OF CHEMICAL RESEARCH (2015)

Review Cell Biology

Histone exchange, chromatin structure and the regulation of transcription

Swaminathan Venkatesh et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Chemistry, Physical

Coarse-grained modeling of DNA curvature

Gordon S. Freeman et al.

JOURNAL OF CHEMICAL PHYSICS (2014)

Article Chemistry, Physical

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

Tsuyoshi Terakawa et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Multidisciplinary Sciences

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

Wenfei Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

Structural Analysis of the Hexasome, Lacking One Histone H2A/H2B Dimer from the Conventional Nucleosome

Yasuhiro Arimura et al.

BIOCHEMISTRY (2012)

Article Biophysics

Multiscale Ensemble Modeling of Intrinsically Disordered Proteins: p53 N-Terminal Domain

Tsuyoshi Terakawa et al.

BIOPHYSICAL JOURNAL (2011)

Article Chemistry, Physical

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

Hiroo Kenzaki et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Biochemistry & Molecular Biology

Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence

Dileep Vasudevan et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Biochemistry & Molecular Biology

The Histone Chaperone Nap1 Promotes Nucleosome Assembly by Eliminating Nonnucleosomal Histone DNA Interactions

Andrew J. Andrews et al.

MOLECULAR CELL (2010)

Article Chemistry, Physical

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

Slimane Doudou et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Article Biochemistry & Molecular Biology

A Thermodynamic Model for Nap1-Histone Interactions

Andrew J. Andrews et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Biochemistry & Molecular Biology

A β-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1

Young-Jun Park et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Biochemistry & Molecular Biology

On the mechanism of nucleosome assembly by histone chaperone NAP1

Jacek Mazurkiewicz et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Article Multidisciplinary Sciences

Chromatin remodeling by nucleosome disassembly in vitro

Y Lorch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

The structure of nucleosome assembly protein 1

YJ Park et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

Association states of nucleosome assembly protein 1 and its complexes with histones

KF Tóth et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding

YJ Park et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Preferential binding of the histone (H3-H4)2 tetramer by NAP1 is mediated by the amino-terminal histone tails

SJ McBryant et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution

CA Davey et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)