4.6 Article

Nucleosome assembly and disassembly pathways in vitro

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Measuring DNA mechanics on the genome scale

Aakash Basu et al.

Summary: Mechanical deformations of DNA, such as bending, are common and have been implicated in various cellular functions. A high-throughput assay called 'loop-seq' was developed to measure DNA looping propensity and intrinsic cyclizabilities of DNA fragments across different genomic regions. The study found regions of low bendability in nucleosome-depleted regions, which affects nucleosome sliding and gene transcription. Overall, the study shows that local DNA mechanics have broad functional implications on chromatin organization and transcription.

NATURE (2021)

Review Biochemistry & Molecular Biology

Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention

Ann K. Hogan et al.

Summary: The eukayrotic genome is packaged into chromatin, with nucleosomes being the basic unit composed of DNA and histones. Histones, stable protein species in mammalian cells, play a crucial role in homeostasis. While histones are generally stable, their degradation is necessary in specific conditions for organismal and cellular fitness.

MOLECULAR AND CELLULAR BIOLOGY (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

Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET

Kathrin Lehmann et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends

Ramachandran Boopathi et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Biochemistry & Molecular Biology

Nucleosomes as allosteric scaffolds for genetic regulation

Shoji Takada et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

A dynamic view of DNA structure within the nucleosome: Biological implications

Romain Retureau et al.

JOURNAL OF STRUCTURAL BIOLOGY (2020)

Review Biochemistry & Molecular Biology

Mechanistic and structural insights into histone H2A-H2B chaperone in chromatin regulation

Yan Huang et al.

BIOCHEMICAL JOURNAL (2020)

Review Biochemistry & Molecular Biology

Perspective Primary Role of the Nucleosome

Roger D. Kornberg et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Slow motions in A•T rich DNA sequence

A. Ben Imeddourene et al.

SCIENTIFIC REPORTS (2020)

Review Biochemistry & Molecular Biology

The histone chaperoning pathway: from ribosome to nucleosome

Alonso J. Pardal et al.

DNA PACKAGING: NUCLEOSOME AND CHROMATIN (2019)

Article Biochemistry & Molecular Biology

DNA sequence influences hexasome orientation to regulate DNA accessibility

Matthew Brehove et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Biochemistry & Molecular Biology

Nucleosome structure and dynamics are coming of age

Keda Zhou et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Histone octamer rearranges to adapt to DNA unwrapping

Silvija Bilokapic et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Histone octamer rearranges to adapt to DNA unwrapping

Silvija Bilokapic et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Article Chemistry, Physical

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution

Ahmad Elbahnsi et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Review Genetics & Heredity

H3-H4 Histone Chaperone Pathways

Prerna Grover et al.

ANNUAL REVIEW OF GENETICS, VOL 52 (2018)

Article Biophysics

Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles

Alexander W. Mauney et al.

BIOPHYSICAL JOURNAL (2018)

Article Multidisciplinary Sciences

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

Alexander Gansen et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

Yujie Chen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemistry & Molecular Biology

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers

Franziska Kriegel et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Daiki Kato et al.

SCIENCE (2017)

Article Biochemistry & Molecular Biology

Capitalizing on disaster: Establishing chromatin specificity behind the replication fork

Srinivas Ramachandran et al.

BIOESSAYS (2017)

Article Biochemistry & Molecular Biology

Single-Molecule Investigations on Histone H2A-H2B Dynamics in the Nucleosome

Jaehyoun Lee et al.

BIOCHEMISTRY (2017)

Article Multidisciplinary Sciences

High-resolution biophysical analysis of the dynamics of nucleosome formation

Akiko Hatakeyama et al.

SCIENTIFIC REPORTS (2016)

Article Biochemistry & Molecular Biology

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

Thuy T. M. Ngo et al.

Article Biochemistry & Molecular Biology

Revealing transient structures of nucleosomes as DNA unwinds

Yujie Chen et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

Histone- and DNA sequence-dependent stability of nucleosomes studied by single-pair FRET

Katalin Toth et al.

CYTOMETRY PART A (2013)

Article Multidisciplinary Sciences

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

Maxim Y. Sheinin et al.

NATURE COMMUNICATIONS (2013)

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 Biochemistry & Molecular Biology

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

Lacramioara Bintu et al.

Article Biochemistry & Molecular Biology

The mechanics behind DNA sequence-dependent properties of the nucleosome

Eugene Y. D. Chua et al.

NUCLEIC ACIDS RESEARCH (2012)

Review Biochemistry & Molecular Biology

Structural dynamics of nucleosomes at single-molecule resolution

John S. Choy et al.

TRENDS IN BIOCHEMICAL SCIENCES (2012)

Article Biochemistry & Molecular Biology

Dynamics of Nucleosomes Assessed with Time-Lapse High-Speed Atomic Force Microscopy

Atsushi Miyagi et al.

BIOCHEMISTRY (2011)

Article Biochemistry & Molecular Biology

Dynamics of Nucleosome Invasion by DNA Binding Proteins

Hannah S. Tims et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Nucleosome accessibility governed by the dimer/tetramer interface

Vera Boehm et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Intrinsic flexibility of B-DNA: the experimental TRX scale

Brahim Heddi et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Single-molecule derivation of salt dependent base-pair free energies in DNA

Josep M. Huguet et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

Michael A. Hall et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

Article Multidisciplinary Sciences

Nucleosome disassembly intermediates characterized by single-molecule FRET

Alexander Gansen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biophysics

Sequence-dependent variations associated with H(2)A/H2B depletion of nucleosomes

L. Kelbauskas et al.

BIOPHYSICAL JOURNAL (2008)

Article Biochemistry & Molecular Biology

Protein-protein forster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z

Duane A. Hoch et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Multidisciplinary Sciences

Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer

M Tomschik et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Characterization of sequence variability in nucleosome core histone folds

SA Sullivan et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)