Literature DB >> 27434579

Geometric control and modeling of genome reprogramming.

Caroline Uhler1, G V Shivashankar2,3.   

Abstract

Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.

Keywords:  cell geometry; chromosome organization; gene expression; nuclear morphology; sphere packing models

Mesh：

Substances：

Year:  2016        PMID： 27434579      PMCID： PMC6085119          DOI： 10.1080/19490992.2016.1201620

Source DB:  PubMed          Journal:  Bioarchitecture        ISSN： 1949-0992


  43 in total

Review 1.  Micropatterning as a tool to decipher cell morphogenesis and functions.

Authors:  Manuel Théry
Journal:  J Cell Sci       Date:  2010-12-15       Impact factor: 5.285

Review 2.  Tissue cells feel and respond to the stiffness of their substrate.

Authors:  Dennis E Discher; Paul Janmey; Yu-Li Wang
Journal:  Science       Date:  2005-11-18       Impact factor: 47.728

Review 3.  Epigenetics: a landscape takes shape.

Authors:  Aaron D Goldberg; C David Allis; Emily Bernstein
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

Review 4.  Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

Review 5.  Genome architecture: domain organization of interphase chromosomes.

Authors:  Wendy A Bickmore; Bas van Steensel
Journal:  Cell       Date:  2013-03-14       Impact factor: 41.582

6.  Active genes dynamically colocalize to shared sites of ongoing transcription.

Authors:  Cameron S Osborne; Lyubomira Chakalova; Karen E Brown; David Carter; Alice Horton; Emmanuel Debrand; Beatriz Goyenechea; Jennifer A Mitchell; Susana Lopes; Wolf Reik; Peter Fraser
Journal:  Nat Genet       Date:  2004-09-07       Impact factor: 38.330

Review 7.  Appreciating force and shape—the rise of mechanotransduction in cell biology.

Authors:  Thomas Iskratsch; Haguy Wolfenson; Michael P Sheetz
Journal:  Nat Rev Mol Cell Biol       Date:  2014-10-30       Impact factor: 113.915

8.  Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes.

Authors:  Andreas Bolzer; Gregor Kreth; Irina Solovei; Daniela Koehler; Kaan Saracoglu; Christine Fauth; Stefan Müller; Roland Eils; Christoph Cremer; Michael R Speicher; Thomas Cremer
Journal:  PLoS Biol       Date:  2005-04-26       Impact factor: 8.029

9.  Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes.

Authors:  K Venkatesan Iyer; Shovamayee Maharana; Soumya Gupta; Albert Libchaber; Tsvi Tlusty; G V Shivashankar
Journal:  PLoS One       Date:  2012-10-01       Impact factor: 3.240

10.  A high-resolution map of the three-dimensional chromatin interactome in human cells.

Authors:  Fulai Jin; Yan Li; Jesse R Dixon; Siddarth Selvaraj; Zhen Ye; Ah Young Lee; Chia-An Yen; Anthony D Schmitt; Celso A Espinoza; Bing Ren
Journal:  Nature       Date:  2013-10-20       Impact factor: 49.962
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  5 in total

Review 1.  A potential role for genome structure in the translation of mechanical force during immune cell development.

Authors:  Elsie Jacobson; Jo K Perry; David S Long; Mark H Vickers; Justin M O'Sullivan
Journal:  Nucleus       Date:  2016-09-27       Impact factor: 4.197

2.  Paradoxical Behavior of Oncogenes Undermines the Somatic Mutation Theory.

Authors:  Noemi Monti; Roberto Verna; Aurora Piombarolo; Alessandro Querqui; Mariano Bizzarri; Valeria Fedeli
Journal:  Biomolecules       Date:  2022-04-30

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

Authors:  Elsie C Jacobson; Jo K Perry; David S Long; Ada L Olins; Donald E Olins; Bryon E Wright; Mark H Vickers; Justin M O'Sullivan
Journal:  BMC Biol       Date:  2018-11-26       Impact factor: 7.431

4.  Transcriptional Homeostasis of Oxidative Stress-Related Pathways in Altered Gravity.

Authors:  Svantje Tauber; Swantje Christoffel; Cora Sandra Thiel; Oliver Ullrich
Journal:  Int J Mol Sci       Date:  2018-09-18       Impact factor: 5.923

5.  Rapid coupling between gravitational forces and the transcriptome in human myelomonocytic U937 cells.

Authors:  Cora S Thiel; Svantje Tauber; Swantje Christoffel; Andreas Huge; Beatrice A Lauber; Jennifer Polzer; Katrin Paulsen; Hartwin Lier; Frank Engelmann; Burkhard Schmitz; Andreas Schütte; Christiane Raig; Liliana E Layer; Oliver Ullrich
Journal:  Sci Rep       Date:  2018-09-05       Impact factor: 4.379
  5 in total

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