6,598 results match your criteria chromatin structures


Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures.

Genome Biol 2021 May 11;22(1):150. Epub 2021 May 11.

Institut Pasteur, Imaging and Modeling Unit, UMR 3691, CNRS, Paris, France.

Background: The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chromosomes into epigenetically defined active and repressed compartments and smaller "topologically associated" domains. These domains are often associated with chromatin loops, which largely disappear upon removal of cohesin. Read More

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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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Genetic and Histopathological Alterations in Caco-2 and HuH-7 Cells Treated with Secondary Metabolites of Marine fungi.

J Gastrointest Cancer 2021 May 11. Epub 2021 May 11.

Department of Botany and Microbiology, Faculty of Science, Al-Azhar Uniersity, 11847, Nasr City, Cairo, Egypt.

The present work aimed to study the activity of naturally derived fungal secondary metabolites as anticancer agents concerning their cytotoxicity, apoptotic, genetic, and histopathological profile. It was noticed that Aspergillus terreus, Aspergillus flavus, and Aspergillus fumigatus induced variable toxic potential that was cell type, secondary metabolite type, and concentration dependent. Human colonic adenocarcinoma cells (Caco-2) showed less sensitivity than hepatocyte-derived cellular carcinoma cells (HuH-7), and in turn, the half-maximal inhibitory concentration (IC) was variable. Read More

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Slaying the last unicorn: discovery of histones in the microalga .

R Soc Open Sci 2021 Feb 10;8(2):202023. Epub 2021 Feb 10.

Medical Research Council London Institute of Medical Sciences, London, UK.

Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3 and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes. In the early 1980s, however, a series of biochemical investigations failed to find evidence for histones or nucleosomal structures in the microscopic green alga . Read More

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February 2021

IGF-1R nuclear import and recruitment to chromatin involves both alpha and beta subunits.

Discov Oncol 2021 29;12(1):13. Epub 2021 Apr 29.

Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.

Mature type 1 insulin-like growth factor receptors (IGF-1Rs) are heterotetrameric structures comprising two extracellular α-subunits disulphide-bonded to two transmembrane β-subunits with tyrosine kinase activity. IGF-1R is a well-known cell surface mediator of malignant growth, with an incompletely understood role upon nuclear import as a transcriptional regulator. Previous characterisation of nuclear IGF-1R focused on IGF-1Rβ. Read More

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Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.

Nat Methods 2021 May 7;18(5):482-490. Epub 2021 May 7.

Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy.

Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. Read More

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Promoter G-quadruplex folding precedes transcription and is controlled by chromatin.

Genome Biol 2021 May 7;22(1):143. Epub 2021 May 7.

Li Ka Shing Centre, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.

Background: Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state.

Results: Transcriptional inhibition by DRB or by triptolide reveals that promoter G4 formation, as assessed by G4 ChIP-seq, does not depend on transcriptional activity. Read More

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Effects of Porcine Immature Oocyte Vitrification on Actin Microfilament Distribution and Chromatin Integrity During Early Embryo Development .

Front Cell Dev Biol 2021 19;9:636765. Epub 2021 Apr 19.

Department of Biology of Reproduction, Metropolitan Autonomous University-Iztapalapa, Mexico City, Mexico.

Vitrification is mainly used to cryopreserve female gametes. This technique allows maintaining cell viability, functionality, and developmental potential at low temperatures into liquid nitrogen at -196°C. For this, the addition of cryoprotectant agents, which are substances that provide cell protection during cooling and warming, is required. 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 hierarchical packing of euchromatin domains can be described as multiplicative cascades.

PLoS Comput Biol 2021 May 5;17(5):e1008974. Epub 2021 May 5.

Institute of Biological and Chemical Systems, Dept. Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.

The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such hierarchical packing is equally visible in super-resolution microscopy images of large-scale chromatin organization. Read More

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Integrative analysis reveals unique structural and functional features of the Smc5/6 complex.

Proc Natl Acad Sci U S A 2021 May;118(19)

Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;

Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for the distinct functions of Smc5/6 is poorly understood. Read More

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Mol Pharmacol 2021 May 3. Epub 2021 May 3.

Biosciences Institute, Newcastle University, United Kingdom

DNA topoisomerase II (TOP2) poisons induce protein-DNA crosslinks termed TOP2-DNA covalent complexes, in which TOP2 remains covalently bound to each end of an enzyme-induced double strand DNA break (DSB) via a 5'-phosphotyrosyl bond. Repair of the enzyme-induced DSB first requires the removal of the TOP2 protein adduct which, among other mechanisms, can be accomplished through the proteasomal degradation of TOP2. VCP/p97 is a AAA ATPase which utilises energy from ATP hydrolysis to unfold protein substrates, which can facilitate proteasomal degradation by extracting target proteins from certain cellular structures (such as chromatin) and/or by aiding their translocation into the proteolytic core of the proteasome. 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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The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination.

Int J Mol Sci 2021 Apr 14;22(8). Epub 2021 Apr 14.

iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.

Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3. Read More

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RAD51 Inhibition Induces R-Loop Formation in Early G1 Phase of the Cell Cycle.

Int J Mol Sci 2021 Apr 3;22(7). Epub 2021 Apr 3.

Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic.

R-loops are three-stranded structures generated by annealing of nascent transcripts to the template DNA strand, leaving the non-template DNA strand exposed as a single-stranded loop. Although R-loops play important roles in physiological processes such as regulation of gene expression, mitochondrial DNA replication, or immunoglobulin class switch recombination, dysregulation of the R-loop metabolism poses a threat to the stability of the genome. A previous study in yeast has shown that the homologous recombination machinery contributes to the formation of R-loops and associated chromosome instability. Read More

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The JMJ29 Protein Controls Circadian Oscillation through Diurnal Histone Demethylation at the and Loci.

Genes (Basel) 2021 Apr 5;12(4). Epub 2021 Apr 5.

Department of Chemistry, Seoul National University, Seoul 08826, Korea.

The circadian clock matches various biological processes to diurnal environmental cycles, such as light and temperature. Accumulating evidence shows that chromatin modification is crucial for robust circadian oscillation in plants, although chromatin modifiers involved in regulating core clock gene expression have been limitedly investigated. Here, we report that the Jumonji C domain-containing histone demethylase JMJ29, which belongs to the JHDM2/KDM3 group, shapes rhythmic changes in H3K4me3 histone marks at core clock loci in . 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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Metallobiochemistry of ultratrace levels of bismuth in the rat II. Interaction of Bi with tissue, intracellular and molecular components.

J Trace Elem Med Biol 2021 Apr 20:126752. Epub 2021 Apr 20.

Department of Physics, Università Degli Studi di Milano, Via Celoria 16, Milano, I-20133, Italy; LASA, Department of Physics, Università Degli Studi di Milano and INFN-Milano, Via F.lli Cervi 201, Segrate, MI, I-20090, Italy. Electronic address:

Background: Knowledge on Bi metabolism in laboratory animals refers to studies at "extreme" exposures, i.e. pharmacologically relevant high-doses (mg kg b. Read More

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HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells.

Elife 2021 Apr 27;10. Epub 2021 Apr 27.

Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.

HIV-1 replication commences inside the cone-shaped viral capsid, but timing, localization and mechanism of uncoating are under debate. We adapted a strategy to visualize individual reverse-transcribed HIV-1 cDNA molecules and their association with viral and cellular proteins using fluorescence and correlative-light-and-electron-microscopy (CLEM). We specifically detected HIV-1 cDNA inside nuclei, but not in the cytoplasm. Read More

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The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers.

Comput Struct Biotechnol J 2021 26;19:1684-1693. Epub 2021 Mar 26.

Beijing Institute of Radiation Medicine, Beijing 100850, China.

Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a "TAD hierarchical score (TH score)" for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. Read More

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Visualization Ability of Phase-Contrast Synchrotron-Based X-Ray Imaging Using an X-Ray Interferometer in Soft Tissue Tumors.

Technol Cancer Res Treat 2021 Jan-Dec;20:15330338211010121

School of Allied Health Sciences, Kitasato University, Sagamihara, Kanagawa, Japan.

Phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer provides high sensitivity and high spatial resolution, and it has the ability to depict the fine morphological structures of biological soft tissues, including tumors. In this study, we quantitatively compared phase-contrast synchrotron-based X-ray computed tomography images and images of histopathological hematoxylin-eosin-stained sections of spontaneously occurring rat testicular tumors that contained different types of cells. The absolute densities measured on the phase-contrast synchrotron-based X-ray computed tomography images correlated well with the densities of the nuclear chromatin in the histological images, thereby demonstrating the ability of phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer to reliably identify the characteristics of cancer cells within solid soft tissue tumors. Read More

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Broadening our understanding of genetic risk for scleroderma/systemic sclerosis by querying the chromatin architecture surrounding the risk haplotypes.

BMC Med Genomics 2021 Apr 24;14(1):114. Epub 2021 Apr 24.

Quantitative Systems Pharmacology, Enhanced Pharmacodynamics, LLC, Buffalo, NY, USA.

Background: Genetic variants in the human leukocyte antigen (HLA) locus contribute to the risk for developing scleroderma/systemic sclerosis (SSc). However, there are other replicated loci that also contribute to genetic risk for SSc, and it is unknown whether genetic risk in these non-HLA loci acts primarily on the vasculature, immune system, fibroblasts, or other relevant cell types. We used the Cistrome database to investigate the epigenetic landscapes surrounding 11 replicated SSc associated loci to determine whether SNPs in these loci may affect regulatory elements and whether they are likely to impact a specific cell type. Read More

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Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life.

Mol Ecol Resour 2021 Apr 23. Epub 2021 Apr 23.

State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.

Butterfly hillstream loach (Beaufortia kweichowensis), a benthic fish in the torrential mountain streams, possesses a totally flat ventrum, flattened craniofacial and body skeletons, and enlarged paired fins covered by substantially small keratinous structures. However, little is known about the genetic basis of these specialized morphological adaptations. Here we present a 448. Read More

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G-quadruplexes are transcription factor binding hubs in human chromatin.

Genome Biol 2021 Apr 23;22(1):117. Epub 2021 Apr 23.

Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

Background: The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many questions remain on how binding site specificity is governed.

Results: Herein, we reveal a previously unappreciated role for DNA secondary structures as key features for TF recruitment. Read More

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Structural alteration of the nucleus for the reprogramming of gene expression.

FEBS J 2021 Apr 23. Epub 2021 Apr 23.

Graduate School of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan.

The regulation of gene expression is a critical process for establishing and maintaining cellular identity. Gene expression is controlled through a chromatin-based mechanism in the nucleus of eukaryotic cells. Recent studies suggest that chromatin accessibility and the higher-order structure of chromatin affect transcriptional outcome. Read More

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Cell-free fetal DNA coming in all sizes and shapes.

Prenat Diagn 2021 Apr 21. Epub 2021 Apr 21.

Centre for Novostics, Hong Kong Science Park, New Territories, Hong Kong SAR, China.

Cell-free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non-invasively from maternal blood. Through the years, evidence has accumulated to show that cell-free fetal DNA molecules are derived from placental tissues, are mainly of short DNA fragments and have rapid post-delivery clearance profiles. Read More

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Epigenetic insight into regulatory role of chromatin covalent modifications in lifecycle and virulence of Phytophthora.

Environ Microbiol Rep 2021 Apr 19. Epub 2021 Apr 19.

Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES - León, UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.

The Oomycota phylum includes fungi-like filamentous microorganisms classified as plant pathogens. The most destructive genus within oomycetes is Phytophthora, which causes diseases in plants of economic importance in agriculture, forestry, and ornamental. Phytophthora species are widespread worldwide and some of them enable adaptation to different hosts and environmental changes. Read More

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G4detector: Convolutional Neural Network to Predict DNA G-quadruplexes.

IEEE/ACM Trans Comput Biol Bioinform 2021 Apr 19;PP. Epub 2021 Apr 19.

G-quadruplexes (G4s) are nucleic acid secondary structures that form within guanine-rich DNA or RNA sequences. G4 formation can affect chromatin architecture and gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. The experimental data produced by the G4-seq experiment provides unprecedented details on G4 formation in the genome. Read More

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Telomere Replication: Solving Multiple End Replication Problems.

Front Cell Dev Biol 2021 1;9:668171. Epub 2021 Apr 1.

Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Cancer Research Pavilion, Université de Sherbrooke, Sherbrooke, QC, Canada.

Eukaryotic genomes are highly complex and divided into linear chromosomes that require end protection from unwarranted fusions, recombination, and degradation in order to maintain genomic stability. This is accomplished through the conserved specialized nucleoprotein structure of telomeres. Due to the repetitive nature of telomeric DNA, and the unusual terminal structure, namely a protruding single stranded 3' DNA end, completing telomeric DNA replication in a timely and efficient manner is a challenge. Read More

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