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topologically associated domains

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https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#1
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27917893/new-insights-into-molecular-organization-of-human-neuraminidase-1-transmembrane-topology-and-dimerization-ability
#2
Pascal Maurice, Stéphanie Baud, Olga V Bocharova, Eduard V Bocharov, Andrey S Kuznetsov, Charlotte Kawecki, Olivier Bocquet, Beatrice Romier, Laetitia Gorisse, Maxime Ghirardi, Laurent Duca, Sébastien Blaise, Laurent Martiny, Manuel Dauchez, Roman G Efremov, Laurent Debelle
Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139-159 (TM1) and 316-333 (TM2) - as potential transmembrane (TM) domains...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917292/deep-resequencing-of-cftr-in-762-f508del-homozygotes-reveals-clusters-of-non-coding-variants-associated-with-cystic-fibrosis-disease-traits
#3
Briana Vecchio-Pagán, Scott M Blackman, Melissa Lee, Melis Atalar, Matthew J Pellicore, Rhonda G Pace, Arianna L Franca, Karen S Raraigh, Neeraj Sharma, Michael R Knowles, Garry R Cutting
Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5' and 5 kb 3' of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration...
2016: Human Genome Variation
https://www.readbyqxmd.com/read/27900493/mining-the-cicer-arietinum-genome-for-the-mildew-locus-o-mlo-gene-family-and-comparative-evolutionary-analysis-of-the-mlo-genes-from-medicago-truncatula-and-some-other-plant-species
#4
Reena Deshmukh, V K Singh, Brahma Deo Singh
The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn...
November 30, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#5
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27893319/insight-into-the-machinery-that-oils-chromatin-dynamics
#6
Roni H G Wright, Narcis Fernandez-Fuentes, Baldomero Oliva, Miguel Beato
The packaging of genetic information in form of chromatin within the nucleus provides cells with the ability to store and protect massive amounts of information within a compact space. Storing information within chromatin allows selective access to specific DNA sequences by regulating the various levels of chromatin structure from nucleosomes, to chromatin fibers, loops and topological associating domains (TADs) using mechanisms that are being progressively unravelled. However, a relatively unexplored aspect is the energetic cost of changing the chromatin configuration to gain access to DNA information...
November 28, 2016: Nucleus
https://www.readbyqxmd.com/read/27876793/pep-19-modulates-calcium-binding-to-calmodulin-by-electrostatic-steering
#7
Xu Wang, John A Putkey
PEP-19 is a small protein that increases the rates of Ca(2+) binding to the C-domain of calmodulin (CaM) by an unknown mechanism. Although an IQ motif promotes binding to CaM, an acidic sequence in PEP-19 is required to modulate Ca(2+) binding and to sensitize HeLa cells to ATP-induced Ca(2+) release. Here, we report the NMR solution structure of a complex between PEP-19 and the C-domain of apo CaM. The acidic sequence of PEP-19 associates between helices E and F of CaM via hydrophobic interactions. This allows the acidic side chains in PEP-19 to extend toward the solvent and form a negatively charged surface that resembles a catcher's mitt near Ca(2+) binding loop III of CaM...
November 23, 2016: Nature Communications
https://www.readbyqxmd.com/read/27869826/pan-cancer-analysis-of-somatic-copy-number-alterations-implicates-irs4-and-igf2-in-enhancer-hijacking
#8
Joachim Weischenfeldt, Taronish Dubash, Alexandros P Drainas, Balca R Mardin, Yuanyuan Chen, Adrian M Stütz, Sebastian M Waszak, Graziella Bosco, Ann Rita Halvorsen, Benjamin Raeder, Theocharis Efthymiopoulos, Serap Erkek, Christine Siegl, Hermann Brenner, Odd Terje Brustugun, Sebastian M Dieter, Paul A Northcott, Iver Petersen, Stefan M Pfister, Martin Schneider, Steinar K Solberg, Erik Thunissen, Wilko Weichert, Thomas Zichner, Roman Thomas, Martin Peifer, Aslaug Helland, Claudia R Ball, Martin Jechlinger, Rocio Sotillo, Hanno Glimm, Jan O Korbel
Extensive prior research focused on somatic copy-number alterations (SCNAs) affecting cancer genes, yet the extent to which recurrent SCNAs exert their influence through rearrangement of cis-regulatory elements (CREs) remains unclear. Here we present a framework for inferring cancer-related gene overexpression resulting from CRE reorganization (e.g., enhancer hijacking) by integrating SCNAs, gene expression data and information on topologically associating domains (TADs). Analysis of 7,416 cancer genomes uncovered several pan-cancer candidate genes, including IRS4, SMARCA1 and TERT...
November 21, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27867070/the-shh-topological-domain-facilitates-the-action-of-remote-enhancers-by-reducing-the-effects-of-genomic-distances
#9
Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tugce Aktas, Felix Klein, Wolfgang Huber, François Spitz
Gene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression...
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27851967/a-compendium-of-chromatin-contact-maps-reveals-spatially-active-regions-in-the-human-genome
#10
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr, Bing Ren
The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27826147/regulation-of-disease-associated-gene-expression-in-the-3d-genome
#11
Peter Hugo Lodewijk Krijger, Wouter de Laat
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour...
December 2016: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/27796080/white-matter-structural-network-abnormalities-underlie-executive-dysfunction-in-amyotrophic-lateral-sclerosis
#12
Dennis Dimond, Abdullah Ishaque, Sneha Chenji, Dennell Mah, Zhang Chen, Peter Seres, Christian Beaulieu, Sanjay Kalra
Research in amyotrophic lateral sclerosis (ALS) suggests that executive dysfunction, a prevalent cognitive feature of the disease, is associated with abnormal structural connectivity and white matter integrity. In this exploratory study, we investigated the white matter constructs of executive dysfunction, and attempted to detect structural abnormalities specific to cognitively impaired ALS patients. About 18 ALS patients and 22 age and education matched healthy controls underwent magnetic resonance imaging on a 4...
October 31, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27790213/response-of-core-microbial-consortia-to-chronic-hydrocarbon-contaminations-in-coastal-sediment-habitats
#13
Mathilde Jeanbille, Jérôme Gury, Robert Duran, Jacek Tronczynski, Hélène Agogué, Olfa Ben Saïd, Jean-François Ghiglione, Jean-Christophe Auguet
Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs) contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e., Bacteria, Archaea, and Eukarya) using 454 pyrosequencing on the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon) and the French Atlantic Ocean (Bay of Biscay and English Channel)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27771369/mapping-pathogenic-mutations-suggests-an-innovative-structural-model-for-the-pendrin-slc26a4-transmembrane-domain
#14
Claudio Bassot, Giovanni Minervini, Emanuela Leonardi, Silvio C E Tosatto
Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter...
October 19, 2016: Biochimie
https://www.readbyqxmd.com/read/27770004/copy-number-changes-can-create-pathogenic-chromatin-domains
#15
(no author information available yet)
DNA duplications that overlap topologically associated domain (TAD) boundaries can create new TADs.
December 2016: Cancer Discovery
https://www.readbyqxmd.com/read/27766858/solid-state-nmr-investigation-of-the-structural-topology-and-lipid-interactions-of-a-viral-fusion-protein-chimera-containing-the-fusion-peptide-and-transmembrane-domain
#16
Hongwei Yao, Myungwoon Lee, Shu Y Liao, Mei Hong
The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of the parainfluenza virus 5 (PIV5) fusion protein F using solid-state NMR...
October 21, 2016: Biochemistry
https://www.readbyqxmd.com/read/27764097/dynamic-nucleosome-movement-provides-structural-information-of-topological-chromatin-domains-in-living-human-cells
#17
Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi
The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27756106/segment-swapping-aided-the-evolution-of-enzyme-function-the-case-of-uroporphyrinogen-iii-synthase
#18
András Szilágyi, Dániel Györffy, Péter Závodszky
In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism...
October 18, 2016: Proteins
https://www.readbyqxmd.com/read/27745839/structural-chromosomal-rearrangements-require-nucleotide-level-resolution-lessons-from-next-generation-sequencing-in-prenatal-diagnosis
#19
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27739811/plastic-deformation-of-tubular-crystals-by-dislocation-glide
#20
Daniel A Beller, David R Nelson
Tubular crystals, two-dimensional lattices wrapped into cylindrical topologies, arise in many contexts, including botany and biofilaments, and in physical systems such as carbon nanotubes. The geometrical principles of botanical phyllotaxis, describing the spiral packings on cylinders commonly found in nature, have found application in all these systems. Several recent studies have examined defects in tubular crystals associated with crystalline packings that must accommodate a fixed tube radius. Here we study the mechanics of tubular crystals with variable tube radius, with dislocations interposed between regions of different phyllotactic packings...
September 2016: Physical Review. E
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