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Lamin associated domain

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https://www.readbyqxmd.com/read/28424353/constrained-release-of-lamina-associated-enhancers-and-genes-from-the-nuclear-envelope-during-t-cell-activation-facilitates-their-association-in-chromosome-compartments
#1
Michael I Robson, Jose I de Las Heras, Rafal Czapiewski, Aishwarya Sivakumar, Alastair R W Kerr, Eric Schirmer
The 3D organization of the genome changes concomitantly with expression changes during hematopoiesis and immune activation. Studies have focused either on lamina-associated domains (LADs) or on topologically-associated domains (TADs), defined by preferential local chromatin interactions, and chromosome compartments, defined as higher-order interactions between TADs sharing functionally similar states. However, few studies have investigated how these affect one another. To address this, we mapped LADs using Lamin B1-DamID during Jurkat T-cell activation, finding significant genome re-organization at the nuclear periphery dominated by release of loci frequently important for T-cell function...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28423830/bridging-the-semantic-gap-between-diagnostic-histopathology-and-image-analysis
#2
Lamine Traore, Yannick Kergosien, Daniel Racoceanu
With the wider acceptance of Whole Slide Images (WSI) in histopathology domain, automatic image analysis algorithms represent a very promising solution to support pathologist's laborious tasks during the diagnosis process, to create a quantification-based second opinion and to enhance inter-observer agreement. In this context, reference vocabularies and formalization of the associated knowledge are especially needed to annotate histopathology images with labels complying with semantic standards. In this work, we elaborate a sustainable triptych able to bridge the gap between pathologists and image analysis scientists...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28398466/novel-nesprin-1-mutations-associated-with-dilated-cardiomyopathy-cause-nuclear-envelope-disruption-and-defects-in-myogenesis
#3
Can Zhou, Chen Li, Bin Zhou, Huaqin Sun, Victoria Koullourou, Ian Holt, Megan J Puckelwartz, Derek T Warren, Robert Hayward, Ziyuan Lin, Lin Zhang, Glenn E Morris, Elizabeth M McNally, Sue Shackleton, Li Rao, Catherine M Shanahan, Qiuping Zhang
Nesprins-1 and -2 are highly expressed in skeletal and cardiac muscle and together with SUN (Sad1p/UNC84)-domain containing proteins and lamin A/C form the LInker of Nucleoskeleton-and-Cytoskeleton (LINC) bridging complex at the nuclear envelope (NE). Mutations in nesprin-1/2 have previously been found in patients with autosomal dominant Emery-Dreifuss muscular dystrophy (EDMD) as well as dilated cardiomyopathy (DCM). In this study, three novel rare variants (R8272Q, S8381C and N8406K) in the C-terminus of the SYNE1 gene (nesprin-1) were identified in seven DCM patients by mutation screening...
April 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28395088/neuropathological-hallmarks-of-brain-malformations-in-extreme-phenotypes-related-to-dync1h1-mutations
#4
Annie Laquerriere, Camille Maillard, Mara Cavallin, Françoise Chapon, Florent Marguet, Arnaud Molin, Sabine Sigaudy, Marie Blouet, Guillaume Benoist, Carla Fernandez, Karine Poirier, Jamel Chelly, Sophie Thomas, Nadia Bahi-Buisson
Dyneins play a critical role in a wide variety of cellular functions such as the movement of organelles and numerous aspects of mitosis, making it central player in neocortical neurogenesis and migration. Recently, cytoplasmic dynein-1, heavy chain-1 (DYNC1H1) mutations have been found to cause a wide spectrum of brain cortical malformations. We report on the detailed neuropathological features of brain lesions from 2 fetuses aged 36 and 22 weeks of gestation (WG), respectively, carrying de novo DYNC1H1 mutations, p...
March 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28385710/non-random-domain-organization-of-the-arabidopsis-genome-at-the-nuclear-periphery
#5
Xiuli Bi, Yingjuan Cheng, Bo Hu, Xiaoli Ma, Rui Wu, Jiawei Wang, Chang Liu
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the non-random positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants...
April 6, 2017: Genome Research
https://www.readbyqxmd.com/read/28357352/chromatin-binding-and-silencing-two-roles-of-the-same-protein-lem2
#6
COMMENT
Ramón Ramos Barrales, Sigurd Braun
Transcriptionally repressed chromatin localizes to specific areas within the eukaryotic nucleus and is often found at the nuclear periphery, which is thought to provide a specialized compartment for gene silencing. However, the molecular mechanisms that establish this spatial chromatin organization are still poorly understood. In our recent work (Barrales et al. 2016), we identified the nuclear envelope protein Lem2, a homolog of metazoan lamin-associated proteins (LAPs), as a relevant factor for heterochromatin silencing and perinuclear localization in the fission yeast Schizosaccharomyces pombe...
April 4, 2016: Microbial Cell
https://www.readbyqxmd.com/read/28283545/macroh2a-histone-variants-maintain-nuclear-organization-and-heterochromatin-architecture
#7
Julien Douet, David Corujo, Roberto Malinverni, Justine Renauld, Viola Sansoni, Melanija Posavec Marjanović, Neus Cantari'o, Vanesa Valero, Fabien Mongelard, Philippe Bouvet, Axel Imhof, Marc Thiry, Marcus Buschbeck
Genetic loss-of-function studies in development, cancer and somatic cell reprogramming have suggested that the group of macroH2A histone variants might function through stabilizing the differentiated state by a yet unknown mechanism. Here, we present results demonstrating that macroH2A variants have a major function in maintaining nuclear organization and heterochromatin architecture. Specifically, we find that a substantial amount of macroH2A is associated with heterochromatic repeat sequences. We further identify macroH2A on sites of interstitial heterochromatin decorated by H3K9me3...
March 10, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28258187/bi-allelic-variants-in-col3a1-encoding-the-ligand-to-gpr56-are-associated-with-cobblestone-like-cortical-malformation-white-matter-changes-and-cerebellar-cysts
#8
Laura Vandervore, Katrien Stouffs, Ibrahim Tanyalçin, Tim Vanderhasselt, Filip Roelens, Muriel Holder-Espinasse, Agnete Jørgensen, Melanie G Pepin, Florence Petit, Philippe Khau Van Kien, Nadia Bahi-Buisson, Willy Lissens, Alexander Gheldof, Peter H Byers, Anna C Jansen
BACKGROUND: Collagens are one of the major constituents of the pial membrane, which plays a crucial role in neuronal migration and cortical lamination during brain development. Type III procollagen, the chains of which are encoded by COL3A1, is the ligand of the G protein-coupled receptor 56 (GPR56), also known as adhesion G protein-coupled receptor G1. Bi-allelic mutations in GPR56 give rise to cobblestone-like malformation, white matter changes and cerebellar dysplasia. This report shows that bi-allelic mutations in COL3A1 are associated with a similar phenotype...
March 3, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28167501/comprehensive-characterization-of-neutrophil-genome-topology
#9
Yina Zhu, Ke Gong, Matthew Denholtz, Vivek Chandra, Mark P Kamps, Frank Alber, Cornelis Murre
Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains (TADs). However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple TADs. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28137286/chrom3d-three-dimensional-genome-modeling-from-hi-c-and-nuclear-lamin-genome-contacts
#10
Jonas Paulsen, Monika Sekelja, Anja R Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L Sørensen, Corinne Vigouroux, Brigitte Buendia, Philippe Collas
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells...
January 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/28123028/c-terminal-region-truncation-of-reln-disrupts-an-interaction-with-vldlr-causing-abnormal-development-of-the-cerebral-cortex-and-hippocampus
#11
Seungshin Ha, Prem P Tripathi, Anca B Mihalas, Robert F Hevner, David R Beier
We discovered a hypomorphic reelin (Reln) mutant with abnormal cortical lamination and no cerebellar hypoplasia. This mutant, Reln(CTRdel), carries a chemically induced splice-site mutation that truncates the C-terminal region (CTR) domain of RELN protein and displays remarkably distinct phenotypes from reeler The mutant does not have an inverted cortex, but cortical neurons overmigrate and invade the marginal zone, which are characteristics similar to a phenotype seen in the cerebral cortex of Vldlr(null) mice...
January 25, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27986930/c-terminal-region-truncation-of-reln-disrupts-an-interaction-with-vldlr-causing-abnormal-development-of-the-cerebral-cortex-and-hippocampus
#12
Seungshin Ha, Prem P Tripathi, Anca B Mihalas, Robert F Hevner, David R Beier
We discovered a hypomorphic reelin (Reln) mutant with abnormal cortical lamination and no cerebellar hypoplasia. This mutant, Reln (CTRdel), carries a chemically-induced splice-site mutation that truncates the C-terminal region (CTR) domain of RELN protein and displays remarkably distinct phenotypes from reeler The mutant does not have an inverted cortex, but cortical neurons overmigrate and invade the marginal zone, which is similar to a phenotype seen in the cerebral cortex of Vldlr (null) mice. The dentate gyrus shows a novel phenotype; the infrapyramidal blade is absent, while the suprapyramidal blade is present and laminated...
December 16, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27773430/mutations-in-cradd-result-in-reduced-caspase-2-mediated-neuronal-apoptosis-and-cause-megalencephaly-with-a-rare-lissencephaly-variant
#13
Nataliya Di Donato, Ying Y Jean, A Murat Maga, Briana D Krewson, Alison B Shupp, Maria I Avrutsky, Achira Roy, Sarah Collins, Carissa Olds, Rebecca A Willert, Agnieszka M Czaja, Rachel Johnson, Jessi A Stover, Steven Gottlieb, Deborah Bartholdi, Anita Rauch, Amy Goldstein, Victoria Boyd-Kyle, Kimberly A Aldinger, Ghayda M Mirzaa, Anke Nissen, Karlla W Brigatti, Erik G Puffenberger, Kathleen J Millen, Kevin A Strauss, William B Dobyns, Carol M Troy, Robert N Jinks
Lissencephaly is a malformation of cortical development typically caused by deficient neuronal migration resulting in cortical thickening and reduced gyration. Here we describe a "thin" lissencephaly (TLIS) variant characterized by megalencephaly, frontal predominant pachygyria, intellectual disability, and seizures. Trio-based whole-exome sequencing and targeted re-sequencing identified recessive mutations of CRADD in six individuals with TLIS from four unrelated families of diverse ethnic backgrounds. CRADD (also known as RAIDD) is a death-domain-containing adaptor protein that oligomerizes with PIDD and caspase-2 to initiate apoptosis...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27699285/gamma-tubulin-coordinates-nuclear-envelope-assembly-around-chromatin
#14
Catalina Ana Rosselló, Lisa Lindström, Johan Glindre, Greta Eklund, Maria Alvarado-Kristensson
The cytosolic role of γ-tubulin as a microtubule organizer has been studied thoroughly, but its nuclear function is poorly understood. Here, we show that γ-tubulin is located throughout the chromatin of demembranated Xenopus laevis sperm and, as the nucleus is formed, γ-tubulin recruits lamin B3 and nuclear membranes. Immunodepletion of γ-tubulin impairs X. laevis assembly of both the lamina and the nuclear membrane. During nuclear formation in mammalian cell lines, γ-tubulin establishes a cellular protein boundary around chromatin that coordinates nuclear assembly of the daughter nuclei...
September 2016: Heliyon
https://www.readbyqxmd.com/read/27669308/making-sense-of-the-tangle-insights-into-chromatin-folding-and-gene-regulation
#15
REVIEW
Ill-Min Chung, Sarada Ketharnathan, Seung-Hyun Kim, Muthu Thiruvengadam, Mari Kavitha Rani, Govindasamy Rajakumar
Proximity ligation assays such as circularized chromosome conformation capture and high-throughput chromosome capture assays have shed light on the structural organization of the interphase genome. Functional topologically associating domains (TADs) that constitute the building blocks of genomic organization are disrupted and reconstructed during the cell cycle. Epigenetic memory, as well as the sequence of chromosomes, regulate TAD reconstitution. Sub-TAD domains that are invariant across cell types have been identified, and contacts between these domains, rather than looping, are speculated to drive chromatin folding...
September 23, 2016: Genes
https://www.readbyqxmd.com/read/27644504/exploring-the-evolution-of-the-proteins-of-the-plant-nuclear-envelope
#16
Axel Poulet, Aline V Probst, Katja Graumann, Christophe Tatout, David Evans
In this study, we explore the plasticity during evolution of proteins of the higher plant nuclear envelope (NE) from the most ancestral plant species to advanced angiosperms. The higher plant NE contains a functional Linker of Nucleoskeleton and Cytoskeleton (LINC) complex based on conserved Sad1-Unc84 (SUN) domain proteins and plant specific Klarsicht/Anc1/Syne homology (KASH) domain proteins. Recent evidence suggests the presence of a plant lamina underneath the inner membrane and various coiled-coil proteins have been hypothesized to be associated with it including Crowded Nuclei (CRWN; also termed LINC and NMCP), Nuclear Envelope Associated Protein (NEAP) protein families as well as the CRWN binding protein KAKU4...
January 2, 2017: Nucleus
https://www.readbyqxmd.com/read/27641764/a-type-lamins-form-distinct-filamentous-networks-with-differential-nuclear-pore-complex-associations
#17
Wei Xie, Alexandre Chojnowski, Thomas Boudier, John S Y Lim, Sohail Ahmed, Zheng Ser, Colin Stewart, Brian Burke
The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells...
October 10, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27602048/physiological-and-pathological-aging-affects-chromatin-dynamics-structure-and-function-at-the-nuclear-edge
#18
REVIEW
Jérôme D Robin, Frédérique Magdinier
Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27570565/nuclear-lamins-in-cancer
#19
Jerome Irianto, Charlotte R Pfeifer, Irena L Ivanovska, Joe Swift, Dennis E Discher
Dysmorphic nuclei are commonly seen in cancers and provide strong motivation for studying the main structural proteins of nuclei, the lamins, in cancer. Past studies have also demonstrated the significance of microenvironment mechanics to cancer progression, which is extremely interesting because the lamina was recently shown to be mechanosensitive. Here, we review current knowledge relating cancer progression to lamina biophysics. Lamin levels can constrain cancer cell migration in 3D and thereby impede tumor growth, and lamins can also protect a cancer cell's genome...
June 2016: Cellular and Molecular Bioengineering
https://www.readbyqxmd.com/read/27373676/a-novel-nonsense-mutation-in-lmna-gene-identified-by-exome-sequencing-in-an-atrial-fibrillation-family
#20
Jinzhao Zhao, Hong Yao, Zongzhe Li, Li Wang, Guangzong Liu, Dao W Wang, Dao Wen Wang, Zhaoguang Liang
Genetic factor plays an important role in cardiac arrhythmias. Several loci have been identified associated with this disease. However, they only explained parts of it and more genes and loci remain to be identified. In present study, we recruited a four generation family from the north of China. Four members of this family were diagnosed with atrial fibrillation by electrocardiogram (ECG). We used Exome Sequencing and Sanger sequencing to explore the candidate mutation for cardiac arrhythmia in this family...
August 2016: European Journal of Medical Genetics
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