1,599 results match your criteria structures nucleosome


Structural Heterogeneity of Human Histone H2A.1.

J Phys Chem B 2021 May 11. Epub 2021 May 11.

Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States.

Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A. Read More

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Structures and Functions of Chromatin Fibers.

Annu Rev Biophys 2021 05;50:95-116

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; email:

In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. Read More

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Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells.

Nat Commun 2021 05 5;12(1):2524. Epub 2021 May 5.

The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.

Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Read More

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The structure of a virus-encoded nucleosome.

Nat Struct Mol Biol 2021 May 29;28(5):413-417. Epub 2021 Apr 29.

Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.

Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes. Read More

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The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk".

Authors:
Giorgio Bernardi

Life (Basel) 2021 Apr 13;11(4). Epub 2021 Apr 13.

Science Department, Roma Tre University, Viale Marconi 446, 00146 Rome, Italy.

The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two "gene spaces" were found many years ago: A GC-rich, gene-rich "genome core" and a GC-poor, gene-poor "genome desert", the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two "spatial compartments", A and B, identified on the basis of chromatin interactions; and (3) of "forests and prairies" characterized by high and low CpG islands densities. Read More

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ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection.

PLoS Pathog 2021 Apr 28;17(4):e1009567. Epub 2021 Apr 28.

Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America.

Histones are rapidly loaded on the HSV genome upon entry into the nucleus of human fibroblasts, but the effects of histone loading on viral replication have not been fully defined. We showed recently that ATRX is dispensable for de novo deposition of H3 to HSV genomes after nuclear entry but restricted infection through maintenance of viral heterochromatin. To further investigate the roles that ATRX and other histone H3 chaperones play in restriction of HSV, we infected human fibroblasts that were systematically depleted of nuclear H3 chaperones. Read More

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Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures.

Nucleic Acids Res 2021 Apr 20. Epub 2021 Apr 20.

Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.

Transcription elongation can be affected by numerous types of obstacles, such as nucleosome, pausing sequences, DNA lesions and non-B-form DNA structures. Spt4/5 and Elf1 are conserved transcription elongation factors that promote RNA polymerase II (Pol II) bypass of nucleosome and pausing sequences. Importantly, genetic studies have shown that Spt4/5 plays essential roles in the transcription of expanded nucleotide repeat genes associated with inherited neurological diseases. Read More

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Structural basis of nucleosome transcription mediated by Chd1 and FACT.

Nat Struct Mol Biol 2021 Apr 12;28(4):382-387. Epub 2021 Apr 12.

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.

Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. Read More

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Structures of chromatin modulators in complex with nucleosome.

Authors:
Jinrong Min Ke Liu

Curr Opin Chem Biol 2021 Apr 3;63:105-114. Epub 2021 Apr 3.

Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, PR China. Electronic address:

The chromatin structure is dynamically regulated by many different modulators that post-translationally modify histones, replace canonical histones with histone variants, and unwind nucleosomal DNA, thereby modulating the accessibility of nucleosomal DNA and facilitating downstream DNA-templated nuclear processes. To understand how these modulators change the chromatin structure, it is essential to determine the 3D structures of chromatin modulators in complex with nucleosome. Here, we review the very recent progress in structural studies of some selected chromatin modulators in complex with nucleosome, including those of histone demethylases LSD1/2, some pioneer transcription factors, and the PWWP domain-containing protein LEDGF. Read More

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Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force Microscopy.

Front Mol Biosci 2021 10;8:636940. Epub 2021 Mar 10.

Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan.

The atomic force microscopy (AFM) is a powerful tool for imaging structures of molecules bound on surfaces. To gain high-resolution structural information, one often superimposes structure models on the measured images. Motivated by high flexibility of biomolecules, we previously developed a flexible-fitting molecular dynamics (MD) method that allows protein structural changes upon superimposing. Read More

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Beyond the double helix: DNA structural diversity and the PDB.

Authors:
Stephen Neidle

J Biol Chem 2021 Mar 17:100553. Epub 2021 Mar 17.

The School of Pharmacy, University College London, London WC1N 1AX, UK. Electronic address:

The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 67 years. Their structural diversity has extended to the demonstration of sequence-dependent local structure in duplex DNA, to DNA bending in short and long sequences and in the DNA wound round the nucleosome, to left-handed duplex DNAs. Read More

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TagBiFC technique allows long-term single-molecule tracking of protein-protein interactions in living cells.

Commun Biol 2021 Mar 19;4(1):378. Epub 2021 Mar 19.

State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.

Protein-protein interactions (PPIs) are critical for cellular activity regulation. Visualization of PPIs using bimolecular fluorescence complementation (BiFC) techniques helps to understand how PPIs implement their functions. However, current BiFC is based on fluorescent proteins and the brightness and photostability are suboptimal for single molecule tracking experiments, resulting in either low spatiotemporal resolution or incapability of tracking for extended time course. Read More

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Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.

Nat Commun 2021 03 19;12(1):1763. Epub 2021 Mar 19.

Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. Read More

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Reversible chromatin condensation by the DNA repair and demethylation factor thymine DNA glycosylase.

Nucleic Acids Res 2021 03;49(5):2450-2459

Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.

Chromatin structures (and modulators thereof) play a central role in genome organization and function. Herein, we report that thymine DNA glycosylase (TDG), an essential enzyme involved in DNA repair and demethylation, has the capacity to alter chromatin structure directly through its physical interactions with DNA. Using chemically defined nucleosome arrays, we demonstrate that TDG induces decompaction of individual chromatin fibers upon binding and promotes self-association of nucleosome arrays into higher-order oligomeric structures (i. Read More

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The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array.

J Mol Biol 2021 May 2;433(10):166902. Epub 2021 Mar 2.

Department of Physics and the Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL 60616, United States. Electronic address:

Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. Read More

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Single-Molecule Imaging Reveals the Mechanism Underlying Histone Loading of AAA+ ATPase Abo1.

Mol Cells 2021 Feb;44(2):79-87

Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.

Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. Read More

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February 2021

Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways.

Elife 2021 Mar 2;10. Epub 2021 Mar 2.

Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States.

Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 and 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Read More

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Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy.

Chromosome Res 2021 Mar 22;29(1):81-94. Epub 2021 Feb 22.

Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan.

The chromosome compaction of chromatin fibers results in the formation of the nucleosome, which consists of a DNA unit coiled around a core of histone molecules associated with linker histone. The compaction of chromatin fibers has been a topic of controversy since the discovery of chromosomes in the 19th century. Although chromatin fibers were first identified using electron microscopy, the chromatin fibers on the surface of chromosome structures in plants remain unclear due to shrinking and breaking caused by prior chromosome isolation or preparation with alcohol and acid fixation, and critical point drying occurred into dehydration and denatured chromosomal proteins. Read More

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Effects of H2A.B incorporation on nucleosome structures and dynamics.

Biophys J 2021 Apr 18;120(8):1498-1509. Epub 2021 Feb 18.

Department of Physics, Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois. Electronic address:

The H2A.B histone variant is an epigenetic regulator involved in transcriptional upregulation, DNA synthesis, and splicing that functions by replacing the canonical H2A histone in the nucleosome core particle. Introduction of H2A. Read More

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Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection.

Clin Chem 2021 Mar;67(4):621-630

Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.

Background: Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-free DNA (cfDNA) molecules have jagged ends. Read More

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A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins.

Structure 2021 Feb 13. Epub 2021 Feb 13.

Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA. Electronic address:

The extraterminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between the BRD3 ET domain and either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN) or its 22-residue IN tail peptide (IN) alone reveal similar intermolecular three-stranded β-sheet formations. N relaxation studies reveal a 10-residue linker region (IN) tethering the SH3 domain (IN) to the ET-binding motif (IN):ET complex. Read More

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February 2021

Engineering nucleosomes for generating diverse chromatin assemblies.

Nucleic Acids Res 2021 Feb 15. Epub 2021 Feb 15.

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.

Structural characterization of chromatin is challenging due to conformational and compositional heterogeneity in vivo and dynamic properties that limit achievable resolution in vitro. Although the maximum resolution for solving structures of large macromolecular assemblies by electron microscopy has recently undergone profound increases, X-ray crystallographic approaches may still offer advantages for certain systems. One such system is compact chromatin, wherein the crystalline state recapitulates the crowded molecular environment within the nucleus. Read More

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February 2021

Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase.

Life Sci Alliance 2021 04 11;4(4). Epub 2021 Feb 11.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan

SET8 is solely responsible for histone H4 lysine-20 (H4K20) monomethylation, which preferentially occurs in nucleosomal H4. However, the underlying mechanism by which SET8 specifically promotes the H4K20 monomethylation in the nucleosome has not been elucidated. Here, we report the cryo-EM structures of the human SET8-nucleosome complexes with histone H3 and the centromeric H3 variant, CENP-A. Read More

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Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.

JCI Insight 2021 Apr 8;6(7). Epub 2021 Apr 8.

IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France.

To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Read More

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Combinations of histone post-translational modifications.

Biochem J 2021 Feb;478(3):511-532

Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, U.S.A.

Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome. Histone PTMs store and convey complex signals about the state of the genome. Read More

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February 2021

Recent Advances in Histone Glycation: Emerging role in Diabetes and Cancer.

Glycobiology 2021 Feb 6. Epub 2021 Feb 6.

Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, India.

Ever increasing information on genome and proteome has offered fascinating details and new opportunities to understand the molecular biology. It is now known that histone proteins surrounding the DNA play a crucial role in the chromatin structure and function. Histones undergo a plethora of post-translational enzymatic modifications that influence nucleosome dynamics and affect DNA activity. Read More

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February 2021

A Conserved Histone H3-H4 Interface Regulates DNA Damage Tolerance and Homologous Recombination during the Recovery from Replication Stress.

Mol Cell Biol 2021 03 24;41(4). Epub 2021 Mar 24.

Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, Japan

In eukaryotes, genomic DNA is packaged into nucleosomes, which are the basal components coordinating both the structures and functions of chromatin. In this study, we screened a collection of mutations for histone H3/H4 mutants in that affect the DNA damage sensitivity of DNA damage tolerance (DDT)-deficient cells. We identified a class of histone H3/H4 mutations that suppress methyl methanesulfonate (MMS) sensitivity of DDT-deficient cells (referred to here as the histone SDD mutations), which likely cluster on a specific H3-H4 interface of the nucleosomes. Read More

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Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies.

Sci Adv 2021 Jan 8;7(2). Epub 2021 Jan 8.

Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda1-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. Read More

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January 2021

Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction.

Nat Commun 2021 01 29;12(1):714. Epub 2021 Jan 29.

Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Read More

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January 2021

Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome.

Plant Commun 2021 Jan 31;2(1):100140. Epub 2020 Dec 31.

Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China.

Accessible chromatin regions (ACRs) provide physical scaffolds to recruit transcriptional co-regulators and displace their nearby nucleosomes in multiple plant species. Characterization of ACRs and investigation of their biological effects in has lagged behind. Regulation of gene expression relies on the transcriptional co-regulators that are recruited to ACRs to affect epigenomic modifications of surrounding nucleosomes. Read More

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January 2021