Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells

[1]  Daniel S. Day,et al.  Coactivator condensation at super-enhancers links phase separation and gene control , 2018, Science.

[2]  Tao Yu,et al.  RNA polymerase II clustering through CTD phase separation , 2018, bioRxiv.

[3]  Cees Dekker,et al.  Real-time imaging of DNA loop extrusion by condensin , 2018, Science.

[4]  J. Rubin,et al.  Enucleated cells reveal differential roles of the nucleus in cell migration, polarity, and mechanotransduction , 2018, The Journal of cell biology.

[5]  Sydney M. Shaffer,et al.  Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. , 2018, Cell systems.

[6]  Tyler J. Kirby,et al.  Emerging views of the nucleus as a cellular mechanosensor , 2018, Nature Cell Biology.

[7]  Leonid A. Mirny,et al.  Emerging Evidence of Chromosome Folding by Loop Extrusion , 2018, bioRxiv.

[8]  R. Andersson,et al.  Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions , 2017, Nature Communications.

[9]  E. Gomes,et al.  Dealing with the nucleus during cell migration. , 2018, Current opinion in cell biology.

[10]  L. Mirny,et al.  Heterochromatin drives organization of conventional and inverted nuclei , 2018, bioRxiv.

[11]  J. Soutourina Transcription regulation by the Mediator complex , 2017, Nature Reviews Molecular Cell Biology.

[12]  K. Jansen,et al.  Mechanotransduction at the cell-matrix interface. , 2017, Seminars in cell & developmental biology.

[13]  V. Backman,et al.  Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins , 2017, bioRxiv.

[14]  Matteo Pellegrini,et al.  High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure , 2017, Circulation.

[15]  S. Wickström,et al.  Emerging roles of mechanical forces in chromatin regulation , 2017, Journal of Cell Science.

[16]  J. Marko,et al.  Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus , 2017, Molecular biology of the cell.

[17]  M. Merchant,et al.  Frontline Science: Tumor necrosis factor‐α stimulation and priming of human neutrophil granule exocytosis , 2017, Journal of leukocyte biology.

[18]  Mustafa Mir,et al.  Phase separation drives heterochromatin domain formation , 2017, Nature.

[19]  Alma L. Burlingame,et al.  Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin , 2017, Nature.

[20]  Bas van Steensel,et al.  Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.

[21]  Ning Wang Review of cellular mechanotransduction , 2017, Journal of physics D: Applied physics.

[22]  Jacob M. Luber,et al.  HiGlass: web-based visual exploration and analysis of genome interaction maps , 2017, Genome Biology.

[23]  M. Butte,et al.  Cytoskeletal adaptivity regulates T cell receptor signaling , 2017, Science Signaling.

[24]  J. Langowski,et al.  Transcriptomes reflect the phenotypes of undifferentiated, granulocyte and macrophage forms of HL-60/S4 cells , 2017, Nucleus.

[25]  Mathieu Blanchette,et al.  A critical assessment of topologically associating domain prediction tools , 2017, Nucleic acids research.

[26]  R. Young,et al.  A Phase Separation Model for Transcriptional Control , 2017, Cell.

[27]  S. Q. Xie,et al.  Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) , 2017, Nature.

[28]  R. Greenberg,et al.  As a Nucleus Enters a Small Pore, Chromatin Stretches and Maintains Integrity, Even with DNA Breaks. , 2017, Biophysical journal.

[29]  A. Probst,et al.  The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants , 2017, Journal of Cell Science.

[30]  Andrea J. Liu,et al.  DNA Damage Follows Repair Factor Depletion and Portends Genome Variation in Cancer Cells after Pore Migration , 2017, Current Biology.

[31]  R. Alon,et al.  Leukocytes Breach Endothelial Barriers by Insertion of Nuclear Lobes and Disassembly of Endothelial Actin Filaments. , 2017, Cell reports.

[32]  Frank Alber,et al.  Comprehensive characterization of neutrophil genome topology , 2017, bioRxiv.

[33]  R. Kamm,et al.  A Chemomechanical Model for Nuclear Morphology and Stresses during Cell Transendothelial Migration. , 2016, Biophysical journal.

[34]  B. Skinner,et al.  Nuclear morphologies: their diversity and functional relevance , 2016, Chromosoma.

[35]  Ning Wang,et al.  Transcription upregulation via force-induced direct stretching of chromatin , 2016, Nature materials.

[36]  Christoph Dieterich,et al.  Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment , 2016, Nature Cell Biology.

[37]  Caroline Uhler,et al.  Geometric control and modeling of genome reprogramming , 2016, Bioarchitecture.

[38]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[39]  Peter H. L. Krijger,et al.  Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming , 2016, Cell stem cell.

[40]  Jan Lammerding,et al.  Nuclear envelope rupture and repair during cancer cell migration , 2016, Science.

[41]  R. Voituriez,et al.  ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death , 2016, Science.

[42]  M. Brand,et al.  Measurement and Analysis of Extracellular Acid Production to Determine Glycolytic Rate , 2015, Journal of visualized experiments : JoVE.

[43]  Jiaxi Zhou,et al.  Extracellular Acidification Acts as a Key Modulator of Neutrophil Apoptosis and Functions , 2015, PloS one.

[44]  E. Jabbari,et al.  Optimum 3D Matrix Stiffness for Maintenance of Cancer Stem Cells Is Dependent on Tissue Origin of Cancer Cells , 2015, PloS one.

[45]  S. Mochrie,et al.  The tethering of chromatin to the nuclear envelope supports nuclear mechanics , 2015, Nature Communications.

[46]  D. Neal,et al.  Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer , 2015, Oncotarget.

[47]  Philip A. Ewels,et al.  Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C , 2015, Nature Genetics.

[48]  Ramaswamy Krishnan,et al.  Fluid shear, intercellular stress, and endothelial cell alignment. , 2015, American journal of physiology. Cell physiology.

[49]  B. Kc,et al.  Making the LINC: SUN and KASH protein interactions , 2015, Biological chemistry.

[50]  Stephanie L. Hyland,et al.  Identification of active transcriptional regulatory elements with GRO-seq , 2015, Nature Methods.

[51]  Nisha M. Ramdas,et al.  Cytoskeletal control of nuclear morphology and chromatin organization. , 2015, Journal of molecular biology.

[52]  K. Pienta,et al.  Aerobic glycolysis, motility, and cytoskeletal remodeling , 2015, Cell cycle.

[53]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[54]  Yanli Wang,et al.  Topologically associating domains are stable units of replication-timing regulation , 2014, Nature.

[55]  A. Hyman,et al.  Liquid-liquid phase separation in biology. , 2014, Annual review of cell and developmental biology.

[56]  Nutan Srivastava,et al.  Granule Protein Processing and Regulated Secretion in Neutrophils , 2014, Front. Immunol..

[57]  J. Lammerding,et al.  Nuclear Deformability Constitutes a Rate-Limiting Step During Cell Migration in 3-D Environments , 2014, Cellular and molecular bioengineering.

[58]  M. King,et al.  Fluid Shear Stress Increases Neutrophil Activation via Platelet-Activating Factor , 2014, Biophysical journal.

[59]  Philip A. Kramer,et al.  A review of the mitochondrial and glycolytic metabolism in human platelets and leukocytes: Implications for their use as bioenergetic biomarkers , 2014, Redox biology.

[60]  Dennis E. Discher,et al.  Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation , 2013, Science.

[61]  M. Schwab,et al.  DNA Methylation of the SLC16A3 Promoter Regulates Expression of the Human Lactate Transporter MCT4 in Renal Cancer with Consequences for Clinical Outcome , 2013, Clinical Cancer Research.

[62]  G. V. Shivashankar,et al.  Cell geometric constraints induce modular gene-expression patterns via redistribution of HDAC3 regulated by actomyosin contractility , 2013, Proceedings of the National Academy of Sciences.

[63]  Robert M. Hoffman,et al.  Physical limits of cell migration: Control by ECM space and nuclear deformation and tuning by proteolysis and traction force , 2013, The Journal of cell biology.

[64]  Jan Lammerding,et al.  Nuclear Envelope Composition Determines the Ability of Neutrophil-type Cells to Passage through Micron-scale Constrictions* , 2013, The Journal of Biological Chemistry.

[65]  K. Dahl,et al.  Force-induced changes in subnuclear movement and rheology. , 2012, Biophysical journal.

[66]  J. Dekker,et al.  The long-range interaction landscape of gene promoters , 2012, Nature.

[67]  T. Myers,et al.  Accumulation of the Inner Nuclear Envelope Protein Sun1 Is Pathogenic in Progeric and Dystrophic Laminopathies , 2012, Cell.

[68]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[69]  Nicola Elvassore,et al.  Role of YAP/TAZ in mechanotransduction , 2011, Nature.

[70]  K. Dahl,et al.  Nucleoskeleton mechanics at a glance , 2011, Journal of Cell Science.

[71]  Jan Lammerding,et al.  Nuclear mechanics during cell migration. , 2011, Current opinion in cell biology.

[72]  G. Gerlitz,et al.  Efficient cell migration requires global chromatin condensation , 2010, Journal of Cell Science.

[73]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[74]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[75]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[76]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[77]  H. Stenmark Rab GTPases as coordinators of vesicle traffic , 2009, Nature Reviews Molecular Cell Biology.

[78]  Min Han,et al.  SUN1 and SUN2 play critical but partially redundant roles in anchoring nuclei in skeletal muscle cells in mice , 2009, Proceedings of the National Academy of Sciences.

[79]  D. E. Olins,et al.  The LINC-less granulocyte nucleus. , 2009, European journal of cell biology.

[80]  Ferhaan Ahmad,et al.  Lamin A/C haploinsufficiency causes dilated cardiomyopathy and apoptosis-triggered cardiac conduction system disease. , 2008, Journal of molecular and cellular cardiology.

[81]  Bernhard Jenny,et al.  Color Design for the Color Vision Impaired , 2007 .

[82]  S. Sen,et al.  Matrix Elasticity Directs Stem Cell Lineage Specification , 2006, Cell.

[83]  Dennis E Discher,et al.  The nuclear envelope lamina network has elasticity and a compressibility limit suggestive of a molecular shock absorber , 2004, Journal of Cell Science.

[84]  Y. Yoon,et al.  Unexpected Severe Calcification After Transplantation of Bone Marrow Cells in Acute Myocardial Infarction , 2004, Circulation.

[85]  Yuval Kluger,et al.  Gene expression in mature neutrophils: early responses to inflammatory stimuli , 2004, Journal of leukocyte biology.

[86]  G. de Martino,et al.  Cardiac features of Emery-Dreifuss muscular dystrophy caused by lamin A/C gene mutations. , 2003, European heart journal.

[87]  N. Borregaard,et al.  Neutrophil granules and secretory vesicles in inflammation. , 2003, Microbes and infection.

[88]  Donald E Ingber,et al.  Mechanobiology and diseases of mechanotransduction , 2003, Annals of medicine.

[89]  L. Håkansson,et al.  Degranulation of Primary and Secondary Granules in Adherent Human Neutrophils , 2002, Scandinavian journal of immunology.

[90]  D. E. Olins,et al.  Retinoic acid induction of nuclear envelope-limited chromatin sheets in HL-60. , 1998, Experimental cell research.

[91]  H. Dvorak,et al.  Neutrophils Emigrate from Venules by a Transendothelial Cell Pathway in Response to FMLP , 1998, The Journal of experimental medicine.

[92]  L. Kjeldsen,et al.  Mobilization of granules and secretory vesicles during in vivo exudation of human neutrophils. , 1995, Journal of immunology.

[93]  W. Hanlon,et al.  rTNFa Facilitates Human Polymorphonuclear Leukocyte Adherence to Fibrinogen Matrices With Mobilization of Specific and Tertiary but Not Azurophilic Granule Markers , 2005 .

[94]  S. Bloom,et al.  Geographic variation in the incidence of myocardial calcification associated with acute myocardial infarction. , 1989, Human pathology.

[95]  U. Aebi,et al.  The nuclear lamina is a meshwork of intermediate-type filaments , 1986, Nature.

[96]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[97]  G. Gerlitz,et al.  The role of chromatin structure in cell migration. , 2011, Trends in cell biology.

[98]  A. Ignatius,et al.  Mechanotransduktion im Alter und bei Osteoporose , 2010, Osteologie.

[99]  T. Burkholder Mechanotransduction in skeletal muscle. , 2007, Frontiers in bioscience : a journal and virtual library.

[100]  V. Ullrich,et al.  Dependence of neutrophil activation on cell density and adhesion. , 1998, Cell adhesion and communication.

[101]  P. Phatak,et al.  Functional properties of HL60 cells matured with all-trans-retinoic acid and DMSO: differences in response to interleukin-8 and fMLP. , 1995, Leukemia research.