Geometric control and modeling of genome reprogramming

REFERENCES

• Augsten M. Cancer-associated fibroblasts as another polarized cell type of the tumor microenvironment. Front Oncol 2014; 4:62; PMID:24734219; http://dx.doi.org/10.3389/fonc.2014.00062
   PubMedGoogle Scholar
• Bickmore WA, van Steensel B. Genome architecture: domain organization of interphase chromosomes. Cell 2013; 152:1270-84; PMID:23498936; http://dx.doi.org/10.1016/j.cell.2013.02.001
   PubMed Web of Science ®Google Scholar
• Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Muller S, Eils R, Cremer C, Speicher MR. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 2005; 3:e157; PMID:15839726; http://dx.doi.org/10.1371/journal.pbio.0030157
   PubMed Web of Science ®Google Scholar
• Branco MR, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 2006; 4:780; http://dx.doi.org/10.1371/journal.pbio.0040138
   Web of Science ®Google Scholar
• Butcher DT, Alliston T, Weaver VM. A tense situation: forcing tumour progression. Nat Rev Cancer 2009; 9:108-22; PMID:19165226; http://dx.doi.org/10.1038/nrc2544
   PubMed Web of Science ®Google Scholar
• Cavalli G, Misteli T.. Functional implications of genome topology. Nat Struct Mol Biol 2013; 20:290-9; PMID:23463314
   PubMed Web of Science ®Google Scholar
• Conway JH, Sloane NJA. (1998). Sphere Packings, Lattices and Groups. Springer-Verlag, NY, 3rd ed.
   Google Scholar
• de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 2013; 502:499-506; PMID:24153303; http://dx.doi.org/10.1038/nature12753
   PubMed Web of Science ®Google Scholar
• Desprat N, Supatto W, Pouille P-A, Beaurepaire E, Farge E.. Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos. Dev Cell 2008; 15:470-7; PMID:18804441; http://dx.doi.org/10.1016/j.devcel.2008.07.009
   PubMed Web of Science ®Google Scholar
• Discher DE, Janmey P, Wang YL. Tissue cells feel and respond to the stiffness of their substrate. Science 2005; 310:1139-43; PMID:16293750; http://dx.doi.org/10.1126/science.1116995
   PubMed Web of Science ®Google Scholar
• Donev A, Cisse I, Sachs D, Variano EA, Stillinger FH, Connelly R, Torquato S, Chaikin PM. Improving the density of jammed disordered packings using ellipsoids. Science 2004; 303:990-3; PMID:14963324; http://dx.doi.org/10.1126/science.1093010
   PubMed Web of Science ®Google Scholar
• Dupont S, Morsut L, Aragona M, Enzo E, Giulitti S, Cordenonsi M, Zanconato F, Le Digabel J, Forcato M, Bicciato S. Role of YAP/TAZ in mechanotransduction. Nature 2011; 474:179-83; PMID:21654799; http://dx.doi.org/10.1038/nature10137
   PubMed Web of Science ®Google Scholar
• Engler AJ, Sen S, Sweeney HL, Discher DE. Matrix elasticity directs stem cell lineage specification. Cell 2006; 126:677-89; PMID:16923388; http://dx.doi.org/10.1016/j.cell.2006.06.044
   PubMed Web of Science ®Google Scholar
• Fanucchi S, Shibayama Y, Burd S, Weinberg MS, Mhlanga MM. Chromosomal contact permits transcription between coregulated genes. Cell 2013; 155:606-20; PMID:24243018; http://dx.doi.org/10.1016/j.cell.2013.09.051
   PubMed Web of Science ®Google Scholar
• Garcia-Lopez P, Garcia-Marin V, Freire M. The histological slides and drawings of Cajal. Front Neuroanat 2010; 4:1-16; PMID:20161990
   PubMed Web of Science ®Google Scholar
• Goldberg AD, Allis CD, Bernstein E. Epigenetics: a landscape takes shape. Cell 2007; 128:635-8; PMID:17320500; http://dx.doi.org/10.1016/j.cell.2007.02.006
   PubMed Web of Science ®Google Scholar
• Gurdon JB, Melton DA. Nuclear reprogramming in cells. Science 2008; 322:1811-5; PMID:19095934; http://dx.doi.org/10.1126/science.1160810
   PubMed Web of Science ®Google Scholar
• Humphrey JD, Dufresne ER, Schwartz MA. Mechanotransduction and extracellular matrix homeostasis. Nat Rev Mol Cell Bio 2014; 15, 802-12; http://dx.doi.org/10.1038/nrm3896
   PubMed Web of Science ®Google Scholar
• Iskratsch T, Wolfenson H, Sheetz MP. Appreciating force and shape [mdash] the rise of mechanotransduction in cell biology. Nat Rev Mol Cell Bio 2014; 15:825-33; PMID:25355507; http://dx.doi.org/10.1038/nrm3903
   PubMed Web of Science ®Google Scholar
• Iyer KV, Maharana S, Gupta S, Libchaber A, Tlusty T, Shivashankar GV. Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes. PLoS One 2012; 7:e46628; PMID:23049710; http://dx.doi.org/10.1371/journal.pone.0046628
   PubMedGoogle Scholar
• Makhija E, Jokhun DS, Shivashankar GV. Nuclear deformability and telomere dynamics are regulated by cell geometric constraints. Proc Natl Acad Sci USA 2016; 113(1):E32-40; PMID:26699462; http://dx.doi.org/10.1073/pnas.1513189113
   PubMed Web of Science ®Google Scholar
• Iyer KV, Pulford S, Mogilner A, Shivashankar GV. Mechanical activation of cells reveals distinct timescales in chromatin remodeling and MKL nuclear transport Biophys J 2012; 103:1416-28; PMID:23062334; http://dx.doi.org/10.1016/j.bpj.2012.08.041
   PubMed Web of Science ®Google Scholar
• Jain N, Iyer KV, Kumar A, Shivashankar GV. Cell geometric constraints induce modular gene-expression patterns via redistribution of HDAC3 regulated by actomyosin contractility. Proc Natl Acad Sci USA 2013; 110:11349-54; PMID:23798429; http://dx.doi.org/10.1073/pnas.1300801110
   PubMed Web of Science ®Google Scholar
• Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen C-A, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013; 503:290-4; PMID:24141950
   PubMed Web of Science ®Google Scholar
• Kilian KA, Bugarija B, Lahn BT, Mrksich M. Geometric cues for directing the differentiation of mesenchymal stem cells. Proc Natl Acad Sci 2010; 107:4872-7; PMID:20194780; http://dx.doi.org/10.1073/pnas.0903269107
   PubMed Web of Science ®Google Scholar
• Lanctot C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 2007; 8:104-15; PMID:17230197; http://dx.doi.org/10.1038/nrg2041
   PubMed Web of Science ®Google Scholar
• Li Q, Kumar A, Makhija E, Shivashankar GV. The regulation of dynamic mechanical coupling between actin cytoskeleton and nucleus by matrix geometry. Biomaterials 2014; 35:961-9; PMID:24183171; http://dx.doi.org/10.1016/j.biomaterials.2013.10.037
   PubMed Web of Science ®Google Scholar
• Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326:289-93; PMID:19815776; http://dx.doi.org/10.1126/science.1181369
   PubMed Web of Science ®Google Scholar
• Lodi A, Martello S, Monaci M. Two-dimensional packing problems: A survey. European J Oper Res 2003; 141:241-52; http://dx.doi.org/10.1016/S0377-2217(02)00123-6
   Web of Science ®Google Scholar
• Maharana S, Iyer KV, Jain N, Nagarajan M, Wang Y, Shivashankar GV. Chromosome intermingling: The physical basis of chromosome organization in differentiated cells. Nucleic Acids Res 2016; (in press).
   PubMed Web of Science ®Google Scholar
• Mazumder A, Roopa T, Basu A, Mahadevan L, Shivashankar GV. Dynamics of chromatin decondensation reveals the structural integrity of a mechanically prestressed cell nucleus. Biophys J 2008; 95:3028-35; PMID:18556763; http://dx.doi.org/10.1529/biophysj.108.132274
   PubMed Web of Science ®Google Scholar
• Olins DE, Olins AL. Chromatin history: our view from the bridge. Nat Rev Mol Cell Biol 2003; 4:809-14; PMID:14570061; http://dx.doi.org/10.1038/nrm1225
   PubMed Web of Science ®Google Scholar
• Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 2004; 36:1065-71; PMID:15361872; http://dx.doi.org/10.1038/ng1423
   PubMed Web of Science ®Google Scholar
• Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST. The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci USA 2009; 106:6679-84; PMID:19276122; http://dx.doi.org/10.1073/pnas.0900986106
   PubMed Web of Science ®Google Scholar
• Ramdas NM, Shivashankar GV. Cytoskeletal control of nuclear morphology and chromatin organization. J Mol Biol 2015; 427:695-706; PMID:25281900; http://dx.doi.org/10.1016/j.jmb.2014.09.008
   PubMed Web of Science ®Google Scholar
• Rogers CA. Packing and Covering. Volume 54 of Cambridge Tracts in Mathematics and Mathematical Physics. Cambridge, UK: Cambridge University Press; 1964.
   Google Scholar
• Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2009; 42:53-61; PMID:20010836; http://dx.doi.org/10.1038/ng.496
   PubMed Web of Science ®Google Scholar
• Shivashankar GV. Mechanosignaling to cell nucleus and genome regulation. Annu Rev Biophys 2011; 40:361-78; PMID:21391812; http://dx.doi.org/10.1146/annurev-biophys-042910-155319
   PubMed Web of Science ®Google Scholar
• Sun HB, Shen J, Yokota H. Size-dependent positioning of human chromosomes in interphase nuclei. Biophys J 2000; 79:184-190; PMID:10866946; http://dx.doi.org/10.1016/S0006-3495(00)76282-5
   PubMed Web of Science ®Google Scholar
• Talwar S, Jain N, Shivashankar GV. The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity. Biomaterials 2014; 35:2411-9; PMID:24388387; http://dx.doi.org/10.1016/j.biomaterials.2013.12.010
   PubMed Web of Science ®Google Scholar
• Talwar S, Kumar A, Rao M, Menon G, Shivashankar GV. Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells. Biophys J 2013; 104:553-64; PMID:23442906; http://dx.doi.org/10.1016/j.bpj.2012.12.033
   PubMed Web of Science ®Google Scholar
• Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006; 126:663-76; PMID:16904174; http://dx.doi.org/10.1016/j.cell.2006.07.024
   PubMed Web of Science ®Google Scholar
• Théry M.. Micropatterning as a tool to decipher cell morphogenesis and functions. J Cell Sci 2010; 123:4201-13; PMID:21123618; http://dx.doi.org/10.1242/jcs.075150
   PubMed Web of Science ®Google Scholar
• Toh KC, Ramdas N, Shivashankar GV. Actin cytoskeleton differentially alters the dynamics of lamin A/C, HP1α and H2B core histone proteins to remodel chromatin condensation state in living cells. Int. Biology 2015; (in press).
   Google Scholar
• Uhler C, Wright SJ. Packing ellipsoids with overlap. SIAM Rev 2013; 55:671-706; http://dx.doi.org/10.1137/120872309
   Web of Science ®Google Scholar
• Van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat. Biotechnol 2010; 28:1089-95; PMID:20944601; http://dx.doi.org/10.1038/nbt.1680
   PubMed Web of Science ®Google Scholar
• Wang N, Tytell JD, Ingber DE. Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus. Nat Rev Mol Cell Biol 2009; 10:75-82; PMID:19197334; http://dx.doi.org/10.1038/nrm2594
   PubMed Web of Science ®Google Scholar
• Woodcock CL. Chromatin architecture. Curr Opin Struct Biol 2005; 16:1-8.
   Google Scholar