258 results match your criteria nucleosome arrangement

Epigenomic links from metabolism-methionine and chromatin architecture.

Curr Opin Chem Biol 2021 Mar 2;63:11-18. Epub 2021 Mar 2.

Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address:

Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures, including physiological stress, nutritional deprivation, and starvation. Numerous studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure (e.g. Read More

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High-Resolution Mapping of Transcription Initiation in the Asexual Stages of .

Front Cell Infect Microbiol 2020 20;10:617998. Epub 2021 Jan 20.

Whitehead Institute for Biomedical Research, Cambridge, MA, United States.

is a common parasite of humans and animals, causing life-threatening disease in the immunocompromized, fetal abnormalities when contracted during gestation, and recurrent ocular lesions in some patients. Central to the prevalence and pathogenicity of this protozoan is its ability to adapt to a broad range of environments, and to differentiate between acute and chronic stages. These processes are underpinned by a major rewiring of gene expression, yet the mechanisms that regulate transcription in this parasite are only partially characterized. Read More

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January 2021

Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.

Int J Mol Sci 2020 Dec 5;21(23). Epub 2020 Dec 5.

Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.

We analyzed the whole-genome experimental maps of nucleosomes in and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, BoE). Chromatin in 5'-regions of genes we classified on four states according to the hidden Markov model (4HMM). Only the Aquamarine chromatin state we considered as Active, while the rest three states we defined as Non-Active. Read More

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December 2020

The topology of chromatin-binding domains in the NuRD deacetylase complex.

Nucleic Acids Res 2020 12;48(22):12972-12982

The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK.

Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Read More

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December 2020

Massively multiplex single-molecule oligonucleosome footprinting.

Elife 2020 12 2;9. Epub 2020 Dec 2.

Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, United States.

Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. Read More

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December 2020

Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility.

Elife 2020 10 19;9. Epub 2020 Oct 19.

Biophysics Graduate Group, University of California at Berkeley, Berkeley, United States.

Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes, chromatin accessibility and energy expenditure may call for a different framework. Here, we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of by the activator Bicoid and the pioneer-like transcription factor Zelda in living embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate transcription. Read More

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October 2020

Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B.

Nature 2020 10 23;586(7827):151-155. Epub 2020 Sep 23.

Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.

CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core, and they favour the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. Read More

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October 2020

Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame.

Chemistry 2020 Nov 19;26(66):15282-15289. Epub 2020 Oct 19.

Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.

The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. Read More

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November 2020

Megadalton chromatin remodelers: common principles for versatile functions.

Curr Opin Struct Biol 2020 10 6;64:134-144. Epub 2020 Aug 6.

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany. Electronic address:

ATP-dependent chromatin remodelers are enigmatic macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes. Here, we review the recent breakthrough provided by cryo-electron microscopy that reveal the first high-resolution insights into all four families of remodelers. We highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes. Read More

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October 2020

Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.

Nat Struct Mol Biol 2020 02 10;27(2):109-118. Epub 2020 Feb 10.

Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University, Munich, Germany.

Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Read More

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February 2020

Negative supercoil at gene boundaries modulates gene topology.

Nature 2020 01 22;577(7792):701-705. Epub 2020 Jan 22.

IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy.

Transcription challenges the integrity of replicating chromosomes by generating topological stress and conflicts with forks. The DNA topoisomerases Top1 and Top2 and the HMGB family protein Hmo1 assist DNA replication and transcription. Here we describe the topological architecture of genes in Saccharomyces cerevisiae during the G1 and S phases of the cell cycle. Read More

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January 2020

Cryo-EM Structures of Centromeric Tri-nucleosomes Containing a Central CENP-A Nucleosome.

Structure 2020 01 8;28(1):44-53.e4. Epub 2019 Nov 8.

Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Graduate School of Advanced Science & Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address:

The histone H3 variant CENP-A is a crucial epigenetic marker for centromere specification. CENP-A forms a characteristic nucleosome and dictates the higher-order configuration of centromeric chromatin. However, little is known about how the CENP-A nucleosome affects the architecture of centromeric chromatin. Read More

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January 2020

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis.

Genome Biol 2019 08 7;20(1):157. Epub 2019 Aug 7.

Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland.

Background: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Read More

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Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains.

Epigenetics Chromatin 2019 05 13;12(1):28. Epub 2019 May 13.

CNRS, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université, 75005, Paris, France.

Background: Localized functional domains within chromosomes, known as topologically associating domains (TADs), have been recently highlighted. In Drosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the "missing link" between epigenetics and gene activity. Recent observations (Boettiger et al. Read More

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Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene.

Sci Rep 2019 04 9;9(1):5816. Epub 2019 Apr 9.

CIRMM, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan.

By means of Silicon Nano Tweezers (SNTs) the effects on the mechanical properties of λ-phage DNA during interaction with calf thymus nucleosome to form an artificial chromatin analog were measured. At a concentration of 100 nM, a nucleosome solution induced a strong stiffening effect on DNA (1.1 N m). Read More

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Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates.

Sci Rep 2019 02 28;9(1):3072. Epub 2019 Feb 28.

Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, 36390, Vigo, Spain.

Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. Read More

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February 2019

DNA Crookedness Regulates DNA Mechanical Properties at Short Length Scales.

Phys Rev Lett 2019 Feb;122(4):048102

Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

Sequence-dependent DNA conformation and flexibility play a fundamental role in the specificity of DNA-protein interactions. Here we quantify the DNA crookedness: a sequence-dependent deformation of DNA that consists of periodic bends of the base pair centers chain. Using extensive 100  μs-long, all-atom molecular dynamics simulations, we found that DNA crookedness and its associated flexibility are bijective, which unveils a one-to-one relation between DNA structure and dynamics. Read More

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February 2019

A Modular Ligation Strategy for Asymmetric Bivalent Nucleosomes Trimethylated at K36 and K27.

Chembiochem 2019 05 12;20(9):1124-1128. Epub 2019 Mar 12.

Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH B3 485, 1015, Lausanne, Switzerland.

In nature, individual histones in the same nucleosome can carry identical (symmetric) or different (asymmetric) post-translational modification (PTM) patterns, increasing the combinatorial complexity. Embryonic stem cells exhibit "bivalent" nucleosomes, some of which are marked by an asymmetric arrangement of H3K36me3 (an activating PTM) and H3K27me3 (a repressive PTM). Here we describe a modular synthetic method to access such asymmetrically modified nucleosomes and show that H3K36me3 inhibits the activity of the methyltransferase PRC2 locally while still prolonging its chromatin binding time. Read More

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Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in .

Genetics 2019 02 15;211(2):563-578. Epub 2018 Dec 15.

Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403

In the filamentous fungus , constitutive heterochromatin is marked by tri-methylation of histone H3 lysine 9 (H3K9me3) and DNA methylation. We identified mutations in the defective in methylation-1 () gene that cause defects in cytosine methylation and implicate a putative AAA-ATPase chromatin remodeler. Although it was well-established that chromatin remodelers can affect transcription by influencing DNA accessibility with nucleosomes, little was known about the role of remodelers on chromatin that is normally not transcribed, including regions of constitutive heterochromatin. Read More

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February 2019

Cryo-ET reveals the macromolecular reorganization of mitotic chromosomes in vivo.

Proc Natl Acad Sci U S A 2018 10 8;115(43):10977-10982. Epub 2018 Oct 8.

Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 117543, Singapore;

Chromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription. Here, we use cryo-electron tomography (cryo-ET) to determine the 3D arrangement of nuclear macromolecular complexes, including nucleosomes, in frozen-hydrated cells. Read More

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October 2018

Cis-regulatory determinants of MyoD function.

Nucleic Acids Res 2018 08;46(14):7221-7235

Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.

Muscle-specific transcription factor MyoD orchestrates the myogenic gene expression program by binding to short DNA motifs called E-boxes within myogenic cis-regulatory elements (CREs). Genome-wide analyses of MyoD cistrome by chromatin immnunoprecipitation sequencing shows that MyoD-bound CREs contain multiple E-boxes of various sequences. However, how E-box numbers, sequences and their spatial arrangement within CREs collectively regulate the binding affinity and transcriptional activity of MyoD remain largely unknown. Read More

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Fission yeast telosomes: non-canonical histone-containing chromatin structures dependent on shelterin and RNA.

Nucleic Acids Res 2018 09;46(17):8865-8875

Telomere Biology Laboratory, Cancer Research UK, London Research Institute, London, WC2A 3LY, UK.

Despite the prime importance of telomeres in chromosome stability, significant mysteries surround the architecture of telomeric chromatin. Through micrococcal nuclease mapping, we show that fission yeast chromosome ends are assembled into distinct protected structures ('telosomes') encompassing the telomeric DNA repeats and over half a kilobase of subtelomeric DNA. Telosome formation depends on the conserved telomeric proteins Taz1 and Rap1, and surprisingly, RNA. Read More

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September 2018

Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development.

Cell Death Dis 2018 07 9;9(7):765. Epub 2018 Jul 9.

Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, the Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092, China.

The linker histone H1 is critical to maintenance of higher-order chromatin structures and to gene expression regulation. However, H1 dynamics and its functions in embryonic development remain unresolved. Here, we profiled gene expression, nucleosome positions, and H1 locations in early Drosophila embryos. Read More

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Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription.

Mol Cell 2018 07;71(1):89-102.e5

Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva 4, Switzerland. Electronic address:

Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation at eukaryotic promoters. We investigated the mechanistic links between promoter DNA sequence, nucleosome positioning, and transcription. Our results indicate that positioning of the transcription start site-associated +1 nucleosome in yeast is critical for efficient TBP binding and is driven by two key factors, the essential chromatin remodeler RSC and a small set of ubiquitous general regulatory factors (GRFs). Read More

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Histone Chaperone Asf1 Is Required for the Establishment of Repressive Chromatin in Schizosaccharomyces pombe fbp1 Gene Repression.

Mol Cell Biol 2018 09 28;38(18). Epub 2018 Aug 28.

Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan

The arrangement of nucleosomes in chromatin plays a role in transcriptional regulation by restricting the accessibility of transcription factors and RNA polymerase II to -acting elements and promoters. For gene activation, the chromatin structure is altered to an open configuration. The mechanism for this process has been extensively analyzed. Read More

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September 2018

Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.

J Mol Biol 2018 09 27;430(18 Pt B):3093-3110. Epub 2018 Jun 27.

Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Read More

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September 2018

Structure and regulation of the human INO80-nucleosome complex.

Nature 2018 04 11;556(7701):391-395. Epub 2018 Apr 11.

Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK.

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines . Read More

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Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution.

Nucleic Acids Res 2017 Dec;45(22):12739-12751

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interactions (CCIs) from low-resolution Hi-C data. Read More

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December 2017

Chromatin remodeler CHD1 promotes XPC-to-TFIIH handover of nucleosomal UV lesions in nucleotide excision repair.

EMBO J 2017 11 10;36(22):3372-3386. Epub 2017 Oct 10.

Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland

Ultraviolet (UV) light induces mutagenic cyclobutane pyrimidine dimers (CPDs) in nucleosomal DNA that is tightly wrapped around histone octamers. How global-genome nucleotide excision repair (GG-NER) processes CPDs despite that this chromatin arrangement is poorly understood. An increased chromatin association of CHD1 (chromodomain helicase DNA-binding 1) upon UV irradiation indicated possible roles of this chromatin remodeler in the UV damage response. Read More

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November 2017

Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties.

Plant Mol Biol 2017 Sep 24;95(1-2):63-88. Epub 2017 Jul 24.

Division of Plant Biology, Bose Institute, P 1/12 C.I.T. Scheme VII M, Kolkata, 700054, India.

Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. Read More

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September 2017