Molecular Cell Article CentromereTetheringConfinesChromosomeDomains

Jolien Suzanne Verdaasdonk,1 Paula Andrea Vasquez,3 Raymond Mario Barry,1 Timothy Barry,1 Scott Goodwin,1 M. Gregory Forest,2 and Kerry Bloom1,* 1Department of Biology 2Department of Mathematics and Biomedical Engineering University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA 3Department of Mathematics, University of South Carolina, Columbia, SC 29208, USA *Correspondence: kerry_bloom@unc.edu http://dx.doi.org/10.1016/j.molcel.2013.10.021

[1]  Christophe Zimmer,et al.  Principles of chromosomal organization: lessons from yeast , 2011, The Journal of cell biology.

[2]  V. Seitan,et al.  Cohesin and chromatin organisation. , 2012, Current opinion in genetics & development.

[3]  Bas van Steensel,et al.  Genome Architecture: Domain Organization of Interphase Chromosomes , 2013, Cell.

[4]  S. Gasser,et al.  The budding yeast nucleus. , 2010, Cold Spring Harbor perspectives in biology.

[5]  T. Cremer,et al.  Chromosome territories. , 2010, Cold Spring Harbor perspectives in biology.

[6]  D. Spector,et al.  The dynamics of chromosome organization and gene regulation. , 2003, Annual review of biochemistry.

[7]  P. Doyle,et al.  Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent. , 2011, Nano letters.

[8]  W. Bickmore,et al.  Considering Nuclear Compartmentalization in the Light of Nuclear Dynamics , 2003, Cell.

[9]  Christopher M. Austin,et al.  The dynamic landscape of the cell nucleus , 2010, Molecular reproduction and development.

[10]  R. Mazo.  On the theory of brownian motion , 1973 .

[11]  G. Fredrickson.  The theory of polymer dynamics , 1996 .

[12]  Kerry Bloom,et al.  Bub1 Kinase and Sgo1 Modulate Pericentric Chromatin in Response to Altered Microtubule Dynamics , 2012, Current Biology.

[13]  S. Gasser,et al.  Visualizing Chromatin Dynamics in Interphase Nuclei , 2002, Science.

[14]  Xiaohu Wan,et al.  Asymmetric Chromosome Oscillation during Mitosis and Protein Architecture of the Human Kinetochore Measured by K-SHREC (Kinetochore-Speckle High Resolution Co-Localization) , 2008 .

[15]  P. Hastings,et al.  DNA breakage drives nuclear search , 2012, Nature Cell Biology.

[16]  F. Alber,et al.  Physical tethering and volume exclusion determine higher-order genome organization in budding yeast , 2012, Genome research.

[17]  Masaki Sasai,et al.  Dynamical modeling of three-dimensional genome organization in interphase budding yeast. , 2012, Biophysical journal.

[18]  Rodney Rothstein,et al.  Increased chromosome mobility facilitates homology search during recombination , 2012, Nature Cell Biology.

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

[20]  D. Cimini,et al.  The coupling between sister kinetochore directional instability and oscillations in centromere stretch in metaphase PtK1 cells , 2012, Molecular biology of the cell.

[21]  David C. Bouck,et al.  Pericentric Chromatin Is an Elastic Component of the Mitotic Spindle , 2007, Current Biology.

[22]  Theodor Boveri,et al.  Die Blastomerenkerne von Ascaris Megalocephala und die Theorie der Chromosomenindividualität , 1909 .

[23]  Michael Unser,et al.  Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast. , 2008, Genome research.

[24]  Patrick Heun,et al.  Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[25]  K. Bloom.  Beyond the code: the mechanical properties of DNA as they relate to mitosis , 2008, Chromosoma.

[26]  S. Gasser,et al.  Structure and Function in the Budding Yeast Nucleus , 2012, Genetics.

[27]  W. D. Laat,et al.  A Decade of 3c Technologies: Insights into Nuclear Organization References , 2022 .

[28]  O. Gadal,et al.  Nuclear organization and chromatin dynamics in yeast: biophysical models or biologically driven interactions? , 2012, Biochimica et biophysica acta.

[29]  Jean-Christophe Olivo-Marin,et al.  High-resolution statistical mapping reveals gene territories in live yeast , 2008, Nature Methods.

[30]  R. Jessberger,et al.  Cohesin in determining chromosome architecture. , 2012, Experimental cell research.

[31]  T. Misteli,et al.  Mobility and immobility of chromatin in transcription and genome stability. , 2007, Current opinion in genetics & development.

[32]  Kerry Bloom,et al.  Pericentric chromatin loops function as a nonlinear spring in mitotic force balance , 2013, The Journal of cell biology.

[33]  Ralf Everaers,et al.  Structure and Dynamics of Interphase Chromosomes , 2008, PLoS Comput. Biol..

[34]  C. Peterson,et al.  Chromatin dynamics , 2013, Cell cycle.

[35]  Christophe Zimmer,et al.  A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus , 2012, Current Biology.

[36]  M. Martí-Renom,et al.  Chromatin globules: a common motif of higher order chromosome structure? , 2011, Current opinion in cell biology.

[37]  J. Fuchs,et al.  Centromere clustering is a major determinant of yeast interphase nuclear organization. , 2000, Journal of cell science.

[38]  Bruce F. McEwen,et al.  Protein Architecture of the Human Kinetochore Microtubule Attachment Site , 2009, Cell.

[39]  Susan M. Gasser,et al.  Live Imaging of Telomeres yKu and Sir Proteins Define Redundant Telomere-Anchoring Pathways in Yeast , 2002, Current Biology.

[40]  Monika Tsai-Pflugfelder,et al.  Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination. , 2012, Genes & development.

[41]  K. Bloom,et al.  Tension-dependent nucleosome remodeling at the pericentromere in yeast , 2012, Molecular biology of the cell.

[42]  J. Theriot,et al.  Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci , 2012, Proceedings of the National Academy of Sciences.

[43]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[44]  V. Levi,et al.  Mechanical Properties of Organelles Driven by Microtubule-Dependent Molecular Motors in Living Cells , 2011, PloS one.

[45]  Yvonne N Fondufe-Mittendorf,et al.  H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State , 2007, PLoS biology.

[46]  J. Haber,et al.  Lack of chromosome territoriality in yeast: promiscuous rejoining of broken chromosome ends. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Kerry Bloom,et al.  Cohesin, condensin, and the intramolecular centromere loop together generate the mitotic chromatin spring , 2011, The Journal of cell biology.

[48]  Juan J. de Pablo,et al.  Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions , 2002 .

[49]  J. Harden,et al.  Brushlike interactions between thermoresponsive microgel particles. , 2009, Physical review letters.

[50]  T. G. M. Ven,et al.  Measurement of Spring Constants of Polyacrylamide Chains Bridging Particles to a Solid Surface , 1996 .

[51]  Davide Marenduzzo,et al.  Entropic organization of interphase chromosomes , 2009, The Journal of cell biology.

[52]  S. Hadjur,et al.  Cohesin-mediated chromatin interactions--into the third dimension of gene regulation. , 2012, Briefings in functional genomics.

[53]  J. McIntosh,et al.  High-voltage electron tomography of spindle pole bodies and early mitotic spindles in the yeast Saccharomyces cerevisiae. , 1999, Molecular biology of the cell.

[54]  K. Bloom,et al.  Genetic manipulation of centromere function , 1987, Molecular and cellular biology.

[55]  D. Marenduzzo,et al.  Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes , 2010, Chromosome Research.

[56]  Susan M. Gasser,et al.  Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery , 2012, Nature Cell Biology.

[57]  Pamela A Silver,et al.  Motion as a phenotype: the use of live-cell imaging and machine visual screening to characterize transcription-dependent chromosome dynamics , 2006, BMC Cell Biology.

[58]  S. Gasser,et al.  Chromosome Dynamics in the Yeast Interphase Nucleus , 2001, Science.

[59]  Andrea Cocito,et al.  The Replication Checkpoint Protects Fork Stability by Releasing Transcribed Genes from Nuclear Pores , 2011, Cell.

[60]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.