4.7 Review

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Genetics & Heredity

Dynamic alternative DNA structures in biology and disease

Guliang Wang et al.

Summary: Non-B DNA structures play important roles in genetic instability and disease etiology. They affect transcription, replication, recombination, and DNA damage and repair processes. These structures can act as functional genomic elements involved in DNA replication and transcription, chromatin organization, and genome stability. Recent studies have also revealed their role in triggering error-generating DNA repair processes, contributing to genetic variation.

NATURE REVIEWS GENETICS (2023)

Article Biochemistry & Molecular Biology

Role of the histone tails in histone octamer transfer

Yahli Lorch et al.

Summary: The high positive charge of histone tails, which is concentrated in the N- and C-terminal tails, was previously believed to contribute to the stability of nucleosomes. However, we have found that the positive charge actually contributes to instability and plays a crucial role in chromatin remodeling. We have shown that the tails are necessary for histone octamer removal by the RSC chromatin remodeling complex and for histone octamer transfer from nucleosomes to DNA, and this activity is directly related to their positive charge.

NUCLEIC ACIDS RESEARCH (2023)

Article Materials Science, Multidisciplinary

Na+ and K+ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins

Tatyana Andreeva et al.

Summary: This study investigated the differential effects of K+ and Na+ on nucleosome structure, stability, and interactions with protein complexes using single-particle Forster resonance energy transfer microscopy. The results showed that K+ had a maximal stabilizing effect on nucleosome structure at around 80-150 mM, while Na+ had a noticeably lower stabilizing effect. Furthermore, the K+ environment was found to be more preserving for chromatin structure during various nucleosome transactions.

MICROSCOPY AND MICROANALYSIS (2022)

Article Biochemistry & Molecular Biology

H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function

Jian Li et al.

Summary: The Ioc4 subunit of the Isw1b chromatin-remodeling complex interacts with pre-existing histones and DNA through its PWWP domain, facilitating chromatin remodeling during transcription. The Ioc4-PWWP domain promotes efficient remodeling by Isw1b in vitro and maintains ordered chromatin structure in vivo.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

DNA methylation cues in nucleosome geometry, stability and unwrapping

Shuxiang Li et al.

Summary: This study investigates the effects of cytosine methylation at CpG sites on nucleosome dynamics and stability. The results show that methylation induces significant changes in the geometry of DNA, leading to enhanced interactions with the histone octamer and preventing DNA unwrapping.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemical Research Methods

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

Robert C. Mines et al.

Summary: This study investigates the effects of nucleosome-induced pausing on transcriptional dynamics by constructing an agent-based model. The results show that slow nucleosome unwrapping dynamics can induce the formation of RNAPII convoys, preventing nucleosome rebinding and leading to bursts of transcription.

PLOS COMPUTATIONAL BIOLOGY (2022)

Article Biotechnology & Applied Microbiology

Nucleosome positioning based on DNA sequence embedding and deep learning

Guo-Sheng Han et al.

Summary: This study proposes three new deep learning models for nucleosome positioning and finds a better performing integrated model. The models can effectively extract local features and base order features of DNA sequences, providing valuable practical applications.

BMC GENOMICS (2022)

Article Chemistry, Physical

A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions

Tiedong Sun et al.

Summary: Researchers have developed a coarse-grained model of the nucleosome core particle (NCP) using a systematic bottom-up approach. The model accurately reproduces the known structural features of the NCP and provides a realistic description of nucleosome-nucleosome attraction in the presence of multivalent cations. This model opens up possibilities for rigorous modeling of chromatin fibers.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)

Review Cell Biology

Pioneer factors as master regulators of the epigenome and cell fate

Aurelio Balsalobre et al.

Summary: Pioneer factors are transcription factors that can initiate the opening of closed chromatin. They play crucial roles in determining cell fate and cellular reprogramming, but their misexpression can have pathological consequences.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2022)

Article Genetics & Heredity

Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to Functionalize Nucleosomes

Wladyslaw A. Krajewski

Summary: Tight packaging of DNA in chromatin restricts DNA accessibility and dynamics, while studying the inherent dynamics and interactions of nucleosomes is crucial for understanding their functionality and diversifying epigenetic programming methods.

FRONTIERS IN GENETICS (2022)

Article Biochemistry & Molecular Biology

DNA methylation: Precise modulation of chromatin structure and dynamics

Shuxiang Li et al.

Summary: This review summarizes recent experimental and computational studies on the structure, function, and diverse roles of DNA methylation in modulating DNA mechanics, nucleosome and chromatin structure, stability, and dynamics. Additionally, it discusses the relationship between DNA methylation and nucleosome positioning, as well as the crosstalk between DNA methylation and histone tail modifications.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

Article Cell Biology

Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling

Jinsu Kim et al.

Summary: By using signal-dependent transcription factors as perturbation probes, the study of nucleosome dynamics in living cells revealed slower unwrapping dynamics, the necessity for cooperativity in wrapping and unwrapping in fitting the data, the highest eviction probability when the binding site of SDTF is adjacent to the nucleosome dyad, and high location variability with oscillatory SDTF activity.

CELL REPORTS (2022)

Article Biochemistry & Molecular Biology

OCT4 interprets and enhances nucleosome flexibility

Caitlin M. MacCarthy et al.

Summary: Through experiments and molecular simulations, this study reveals how the pioneer factor Oct4 interprets and enhances nucleosome structural flexibility. Oct4 uses its DNA binding domains to propagate and stabilize open nucleosome conformations, providing a structural basis for the versatility of transcription factors' interaction with nucleosomes.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer

Satyanarayan Rao et al.

Summary: Plasma TF footprints can be used to diagnose breast cancer and identify different states and prognosis of tumors. This provides new possibilities for clinical applications.

SCIENCE ADVANCES (2022)

Article Biochemistry & Molecular Biology

Molecular dynamics simulations for the study of chromatin biology

Giovanni B. Brandani et al.

Summary: This review discusses recent molecular dynamics (MD) simulation studies on chromatin biology. It describes the latest method developments and factors affecting the structure and dynamics of chromatin, such as the structural fluctuations of nucleosomes and the organization of chromatin fibers. It also explores the interactions and dynamics of transcription factors on chromatin and how chromatin organization is modulated by molecular motors acting on DNA.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Nucleosomes Meet Their Remodeler Match

Jonathan Markert et al.

Summary: This article discusses the organization of genomic DNA in eukaryotes as arrays of nucleosomes, highlighting the role of ATP-dependent remodelers in modulating nucleosome structure. These remodelers utilize specific nucleosome features to bind and alter nucleosomes, overcoming the barrier posed by the tight interaction between DNA and histones.

TRENDS IN BIOCHEMICAL SCIENCES (2021)

Review Cell Biology

DNA methylation and regulation of gene expression: Guardian of our health

Gaurab Aditya Dhar et al.

Summary: DNA methylation serves as a critical epigenetic mark in higher eukaryotes, regulating gene expression. The methylation pattern in the genome undergoes changes during developmental stages, influenced by interactions between the epigenome, genome, and environmental factors.

NUCLEUS-INDIA (2021)

Review Biophysics

Biophysics of Chromatin Remodeling

Ilana M. Nodelman et al.

Summary: Nucleosomes, as carriers of epigenetic information and gatekeepers of genomic DNA, play a crucial role in the proper growth and development of eukaryotic cells. Chromatin remodelers actively reorganize nucleosomes through ATP-dependent mechanisms, with emerging evidence suggesting twist-based mechanisms for ATP-driven repositioning of nucleosomes along DNA. This review discusses core experimental findings and ideas that have shaped our understanding of how nucleosome sliding may be achieved.

ANNUAL REVIEW OF BIOPHYSICS, VOL 50, 2021 (2021)

Review Biochemistry & Molecular Biology

Breaths, Twists, and Turns of Atomistic Nucleosomes

Jan Huertas et al.

Summary: Gene regulation relies on dynamic changes in chromatin structure, with nucleosomes as the repeating unit controlled by DNA sequence and histone interactions. Molecular dynamics simulations are key for studying chromatin dynamics due to challenges in experimental characterization of nucleosome motions.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Chemistry, Multidisciplinary

Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA

Sevastyan O. Rabdano et al.

Summary: The positively charged N-terminal histone tails interact with nucleosomal DNA, influencing their susceptibility to modifications and recognition by chromatin-binding proteins. The NMR data reveals that H4 tails are dynamically disordered in nucleosomes, showing a reduced conformational flexibility compared to free peptides. The findings suggest a fuzzy interaction between histone H4 tails and nucleosomal DNA, characterized by variable salt bridges and hydrogen bonds.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Multidisciplinary Sciences

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Xinqiang Ding et al.

Summary: The study utilized a near-atomistic model to investigate the structure and dynamics of chromatin, revealing multiple pathways connecting chromatin configurations and influencing the in situ relevance of the 30 nm fiber.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function

Federica Battistini et al.

Summary: The study shows that 5-hydroxymethylation of DNA cytosine leads to stiffer DNA with lower circularization efficiency and reduced ability to form nucleosomes compared to normal cytosine. It disproves the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as 5-hydroxymethylcytosine is even more rigid than 5-methylcytosine. Methylated-DNA binding domains (MBDs) associated with repression activities are sensitive to the substitution of 5-methylcytosine with 5-hydroxymethylcytosine, while MBD3 with dual activation/repression activity is not affected by this change.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Multidisciplinary Sciences

Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions

Stephen E. Farr et al.

Summary: The authors develop a multi-scale chromatin model to investigate the effects of DNA breathing on nucleosome valency, heterogeneity, and dynamics, promoting disordered folding and LLPS.

NATURE COMMUNICATIONS (2021)

Article Chemistry, Multidisciplinary

Tetranucleosome Interactions Drive Chromatin Folding

Walter Alvarado et al.

Summary: The study identifies and characterizes two metastable states, the alpha-tetrahedron and the beta-rhombus, in short chromatin segments, which play important roles in DNA accessibility and local chromatin condensation or elongation. Increases in nucleosome repeat length result in more pronounced structural irregularity and flexibility.

ACS CENTRAL SCIENCE (2021)

Article Biochemistry & Molecular Biology

The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA

Hideaki Ohtomo et al.

Summary: The nucleosome is composed of histone dimers and tetramers, along with DNA, and the dynamic structures of H2A and H2B tails have been studied using NMR and molecular dynamics simulations, revealing different conformations in each nucleosome.

JOURNAL OF MOLECULAR BIOLOGY (2021)

Article Multidisciplinary Sciences

Impact of DNA methylation on 3D genome structure

Diana Buitrago et al.

Summary: This study utilized yeast as a model system lacking DNA methylation machinery to demonstrate the intrinsic effects of methylation on chromatin structure. Despite the absence of machinery for reading and processing methylation marks, induced DNA methylation showed a conserved pattern, indicating its inherent role in modulating chromatin structure.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

Histone tails cooperate to control the breathing of genomic nucleosomes

Jan Huertas et al.

Summary: In this study, the interplay between histone H3 and H2A tails in controlling nucleosome breathing motions is demonstrated through atomistic molecular simulations. The research reveals the mechanisms behind different nucleosome conformations and transitions, emphasizing the significance of histone tails in chromatin dynamics.

PLOS COMPUTATIONAL BIOLOGY (2021)

Article Physics, Fluids & Plasmas

Structural dynamics of DNA depending on methylation pattern

Takeru Kameda et al.

Summary: DNA methylation is associated with biological phenomena and epigenetic regulation, and can alter the mechanical properties of DNA molecules. This study used molecular dynamics simulations to show that methylation patterns affect the local flexibility of DNA, ultimately impacting its overall geometry and stiffness. These findings provide insights into methylation-dependent DNA dynamics in physiological conditions.

PHYSICAL REVIEW E (2021)

Review Biochemistry & Molecular Biology

A Unifying Mechanism of DNA Translocation Underlying Chromatin Remodeling

Lijuan Yan et al.

TRENDS IN BIOCHEMICAL SCIENCES (2020)

Article Chemistry, Physical

Chromatosome Structure and Dynamics from Molecular Simulations

Mehmet Ali Öztürk et al.

Annual Review of Physical Chemistry (2020)

Article Biophysics

Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding

Jan Huertas et al.

BIOPHYSICAL JOURNAL (2020)

Article Biochemistry & Molecular Biology

The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity

Joseph A. Newman et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

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)

Review Biophysics

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Joshua Moller et al.

BIOPHYSICAL JOURNAL (2020)

Article Multidisciplinary Sciences

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

Alicia K. Michael et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Svetlana O. Dodonova et al.

NATURE (2020)

Review Genetics & Heredity

Pioneer Transcription Factors Initiating Gene Network Changes

Kenneth S. Zaret

ANNUAL REVIEW OF GENETICS, VOL 54, 2020 (2020)

Review Biochemistry & Molecular Biology

Perspective Primary Role of the Nucleosome

Roger D. Kornberg et al.

MOLECULAR CELL (2020)

Review Biochemistry & Molecular Biology

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

Andrews Akwasi Agbleke et al.

MOLECULAR CELL (2020)

Article Multidisciplinary Sciences

Nucleosome allostery in pioneer transcription factor binding

Cheng Tan et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

The role of histone tails in nucleosome stability: An electrostatic perspective

Artemi Bendandi et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Review Biophysics

Biophysics of Chromatin Dynamics

Beat Fierz et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 48 (2019)

Article Biochemistry & Molecular Biology

Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling

Lijuan Yan et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biophysics

The Oligomerization Landscape of Histones

Haiqing Zhao et al.

BIOPHYSICAL JOURNAL (2019)

Review Biochemistry & Molecular Biology

Nucleosome remodelling: structural insights into ATP-dependent remodelling enzymes

Ramasubramanian Sundaramoorthy

DNA PACKAGING: NUCLEOSOME AND CHROMATIN (2019)

Article Biochemistry & Molecular Biology

Linking chromatin composition and structural dynamics at the nucleosome level

Grigoriy A. Armeev et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2019)

Article Chemistry, Physical

1CPN: A coarse-grained multi-scale model of chromatin

Joshua Lequieu et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Chemistry, Physical

Cooperative Effects of Cytosine Methylation on DNA Structure and Dynamics

Cecilia Hognon et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

Article Biochemistry & Molecular Biology

Structural Features of Transcription Factors Associating with Nucleosome Binding

Meilin Fernandez Garcia et al.

MOLECULAR CELL (2019)

Review Biochemistry & Molecular Biology

New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation

Takashi Ohyama

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Physics, Multidisciplinary

Theory of Active Chromatin Remodeling

Zhongling Jiang et al.

PHYSICAL REVIEW LETTERS (2019)

Review Genetics & Heredity

Chromatin accessibility and the regulatory epigenome

Sandy L. Klemm et al.

NATURE REVIEWS GENETICS (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

Neutralization of the Positive Charges on Histone Tails by RNA Promotes an Open Chromatin Structure

Rositsa Dueva et al.

CELL CHEMICAL 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)

Review Biochemistry & Molecular Biology

Nucleosome-level 3D organization of the genome

Masae Ohno et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2018)

Review Biochemistry & Molecular Biology

The Human Transcription Factors

Samuel A. Lambert et al.

Article Biochemistry & Molecular Biology

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

Giovanni B. Brandani et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Structural rearrangements of the histone octamer translocate DNA

Silvija Bilokapic et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Multidisciplinary

A sequence environment modulates the impact of methylation on the torsional rigidity of DNA

Johanna Horberg et al.

CHEMICAL COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex

Sebastian Eustermann et al.

NATURE (2018)

Article Multidisciplinary Sciences

The interaction landscape between transcription factors and the nucleosome

Fangjie Zhu et al.

NATURE (2018)

Article Biochemical Research Methods

Inter-nucleosomal communication between histone modifications for nucleosome phasing

Weizhong Chen et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

Nazar Mashtalir et al.

Review Cell Biology

Chromatin and nucleosome dynamics in DNA damage and repair

Michael H. Hauer et al.

GENES & DEVELOPMENT (2017)

Review Cell Biology

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

Cedric R. Clapier et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Multidisciplinary Sciences

In silico evidence for sequence-dependent nudeosome sliding

Joshua Lequieu et al.

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

Article Chemistry, Multidisciplinary

Tension-Dependent Free Energies of Nucleosome Unwrapping

Joshua Lequieu et al.

ACS CENTRAL SCIENCE (2016)

Article Multidisciplinary Sciences

Uncovering the forces between nucleosomes using DNA origami

Jonas J. Funke et al.

SCIENCE ADVANCES (2016)

Article Biochemistry & Molecular Biology

Computational strategies to address chromatin structure problems

Ognjen Perisic et al.

PHYSICAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

The chromatin fiber: multiscale problems and approaches

Gungor Ozer et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)

Article Genetics & Heredity

Histone ubiquitylation and its roles in transcription and DNA damage response

Rithy Meas et al.

DNA REPAIR (2015)

Review Biochemistry & Molecular Biology

The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle

Sonja P. Hergeth et al.

EMBO REPORTS (2015)

Article Multidisciplinary Sciences

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

Benyam Kinde et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Chemistry, Multidisciplinary

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

Gregory D. Bowman et al.

CHEMICAL REVIEWS (2015)

Review Chemistry, Multidisciplinary

Nucleosome Structure and Function

Robert K. McGinty et al.

CHEMICAL REVIEWS (2015)

Article Biochemistry & Molecular Biology

Hydroxymethylation of DNA influences nucleosomal conformation and stability in vitro

Agnes Mendonca et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2014)

Review Cell Biology

Histone core modifications regulating nucleosome structure and dynamics

Peter Tessarz et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2014)

Review Biochemistry & Molecular Biology

Transcribing through the nucleosome

Sheila S. Teves et al.

TRENDS IN BIOCHEMICAL SCIENCES (2014)

Review Biochemistry & Molecular Biology

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

Geeta J. Narlikar et al.

Review Biochemistry & Molecular Biology

Molecular mechanisms of ETS transcription factor-mediated tumorigenesis

Adwitiya Kar et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

Kaifu Chen et al.

GENOME RESEARCH (2013)

Review Multidisciplinary Sciences

The role of the nucleosome acidic patch in modulating higher order chromatin structure

Anna A. Kalashnikova et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2013)

Review Biochemistry & Molecular Biology

DNA methylation dynamics in health and disease

Yehudit Bergman et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Review Neurosciences

DNA Methylation and Its Basic Function

Lisa D. Moore et al.

NEUROPSYCHOPHARMACOLOGY (2013)

Article Biochemistry & Molecular Biology

Selective association between nucleosomes with identical DNA sequences

Jun-ichi Nishikawa et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Probing Allostery Through DNA

Sangjin Kim et al.

SCIENCE (2013)

Article Biochemical Research Methods

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Guillem Portella et al.

PLOS COMPUTATIONAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Contribution of histone N-terminal tails to the structure and stability of nucleosomes

Wakana Iwasaki et al.

FEBS OPEN BIO (2013)

Article Biophysics

The Effect of DNA CpG Methylation on the Dynamic Conformation of a Nucleosome

Isabel Jimenez-Useche et al.

BIOPHYSICAL JOURNAL (2012)

Article Chemistry, Multidisciplinary

Effects of DNA Methylation on the Structure of Nucleosomes

Ju Yeon Lee et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Review Cell Biology

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Karolin Luger et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)

Review Cell Biology

Regulation of chromatin by histone modifications

Andrew J. Bannister et al.

CELL RESEARCH (2011)

Review Biochemistry & Molecular Biology

The dynamics of the nucleosome: thermal effects, external forces and ATP

Ralf Blossey et al.

FEBS JOURNAL (2011)

Article Biochemistry & Molecular Biology

Nucleosomes protect DNA from DNA methylation in vivo and in vitro

Max Felle et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

A quantitative model of nucleosome dynamics

Robert A. Forties et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Cytosine methylation alters DNA mechanical properties

Philip M. D. Severin et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Multidisciplinary Sciences

Histone fold modifications control nucleosome unwrapping and disassembly

Marek Simon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

Till Bartke et al.

Article Chemistry, Multidisciplinary

DNA Methylation Increases Nucleosome Compaction and Rigidity

John S. Choy et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Multidisciplinary Sciences

Relationship between nucleosome positioning and DNA methylation

Ramakrishna K. Chodavarapu et al.

NATURE (2010)

Review Biochemistry & Molecular Biology

Transcription Dynamics

Gordon L. Hager et al.

MOLECULAR CELL (2009)

Article Biochemistry & Molecular Biology

Effects of magnesium and related divalent metal ions in topoisomerase structure and function

Claudia Sissi et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Multidisciplinary Sciences

DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

Steen K. T. Ooi et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Modulation of nucleosome dynamics in Huntington's disease

Edward C. Stack et al.

HUMAN MOLECULAR GENETICS (2007)

Article Biotechnology & Applied Microbiology

The Chd family of chromatin remodelers

Concetta G. A. Marfella et al.

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS (2007)

Article Biochemistry & Molecular Biology

Self-assembly of double-stranded DNA molecules at nanomolar concentrations

Shotaro Inoue et al.

BIOCHEMISTRY (2007)

Article Multidisciplinary Sciences

Histone H4-K16 acetylation controls chromatin structure and protein interactions

M Shogren-Knaak et al.

SCIENCE (2006)

Article Multidisciplinary Sciences

Nucleosome arrays reveal the two-start organization of the chromatin fiber

B Dorigo et al.

SCIENCE (2004)

Review Cell Biology

Chromatin history: our view from the bridge

DE Olins et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2003)

Article Multidisciplinary Sciences

Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF

A Hamiche et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Biophysics

Aggregation of nucleosomes by divalent cations

M de Frutos et al.

BIOPHYSICAL JOURNAL (2001)

Article Biochemistry & Molecular Biology

Role of histone N-terminal tails and their acetylation in nucleosome dynamics

V Morales et al.

MOLECULAR AND CELLULAR BIOLOGY (2000)