Exploring chromatin organization mechanisms through its dynamic properties

References

• Cremer C, Cremer T. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001;2:292-301; PMID:11283701; http://dx.doi.org/10.1038/35066075
   PubMed Web of Science ®Google Scholar
• Lieberman-Aiden E, Berkum NLv, 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
• Bickmore WA, Steensel BV. 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
• Woringer M, Darzacq X, Izeddin I. Geometry of the nucleus: a perspective on gene expression regulation. Curr Opin Chem Biol 2014; 20:112-9; PMID:24981829; http://dx.doi.org/10.1016/j.cbpa.2014.05.009
   PubMed Web of Science ®Google Scholar
• Heard E, Bickmore W. The ins and outs of gene regulation and chromosome territory organization. Curr Opin Cell Biol 2007; 19:31-316; PMID:17184986; http://dx.doi.org/10.1016/j.ceb.2006.12.009
   PubMed Web of Science ®Google Scholar
• Kurz A, Lampel S, Nickolenko JE, Bradl J, Bermer A, Zirbel RM, Cremer T, Lichter P. Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 1996; 135:1195-205; PMID:8947544; http://dx.doi.org/10.1083/jcb.135.5.1195
   PubMed Web of Science ®Google Scholar
• Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 1997; 7:930-9; PMID:9382846; http://dx.doi.org/10.1016/S0960-9822(06)00412-X
   PubMed Web of Science ®Google Scholar
• Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, et al. Chromatin architecture reorganization during stem cell differentiation. Nature 2015; 518:331-6; PMID:25693564; http://dx.doi.org/10.1038/nature14222
   PubMed Web of Science ®Google Scholar
• Soutoglou E, Misteli T. Mobility and immobility of chromatin in transcription and genome stability. Curr Opin Genet Dev 2007; 17:435-42; PMID:17905579; http://dx.doi.org/10.1016/j.gde.2007.08.004
   PubMed Web of Science ®Google Scholar
• Bronshtein I, Kepten E, Kanter I, Berezin S, Lindner M, Redwood AB, Mai S, Gonzalo S, Foisner R, Shav-Tal Y, et al. Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nat Commun 2015; 6:8044; PMID:26299252; http://dx.doi.org/10.1038/ncomms9044
   PubMed Web of Science ®Google Scholar
• Kepten E, Bronshtein I, Garini Y. Improved estimation of anomalous diffusion exponents in single-particle tracking experiments. Phys Rev E 2013; 87:052713; http://dx.doi.org/10.1103/PhysRevE.87.052713
   Google Scholar
• Burnecki K, Kepten E, Janczura J, Bronshtein I, Garini Y, Weron A. Universal algorithm for identification of fractional Brownian motion. A case of telomere subdiffusion. Biophys J 2012; 103:1839-47; PMID:23199912; http://dx.doi.org/10.1016/j.bpj.2012.09.040
   PubMed Web of Science ®Google Scholar
• Barkai E, Garini Y, Metzler R. Strange kinetics of single molecules in living cells. Phys Today 2012; 65:29-35; http://dx.doi.org/10.1063/PT.3.1677
   Web of Science ®Google Scholar
• Thompson RE, Larson DR, Webb WW. Precise nanometer localization analysis for individual fluorescent probes. Biophys J 2002; 82:2775-83; PMID:11964263; http://dx.doi.org/10.1016/S0006-3495(02)75618-X
   PubMed Web of Science ®Google Scholar
• Berger IB, Kepten E, Garini Y. Single-particle tracking for studying the dynamic properties of genomic regions in live cells. Methods Mol Biol 2013;1042:139–51.
   Google Scholar
• Metzler R, Jeon J-H, Cherstvy AG, Barkai E. Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking. Phys Chem Chem Phys 2014; 16:24128-64; PMID:25297814; http://dx.doi.org/10.1039/C4CP03465A
   PubMed Web of Science ®Google Scholar
• Weiss M, Elsner M, Kartberg F, Nilsson T. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys J 2004; 87:3518-24; PMID:15339818; http://dx.doi.org/10.1529/biophysj.104.044263
   PubMed Web of Science ®Google Scholar
• Dechat T, Pfleghaar K, Sengupta K, Shimi T, Shumaker DK, Solimando L, Goldman RD. Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev 2008; 22:832-53; PMID:18381888; http://dx.doi.org/10.1101/gad.1652708
   PubMed Web of Science ®Google Scholar
• Ho CY, Lammerding J. Lamins at a glance. J Cell Sci 2012; 125:2087-93; PMID:22669459; http://dx.doi.org/10.1242/jcs.087288
   PubMed Web of Science ®Google Scholar
• Gruenbaum Y, Foisner R. Lamins: Nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 2015; 84:131-64; PMID:25747401; http://dx.doi.org/10.1146/annurev-biochem-060614-034115
   PubMed Web of Science ®Google Scholar
• Broers JLV, Machiels BM, van Eys GJJM, Kuijpers HJH, Manders EMM, van Driel R, Ramaekers FC. Dynamics of the nuclear lamina as monitored by GFP-tagged A-type lamins. J Cell Sci 1999; 112:3463-75; PMID:10504295
   PubMed Web of Science ®Google Scholar
• Brody Y, Neufeld N, Bieberstein N, Causse SZ, Böhnlein E-M, Neugebauer KM, Darzacq X, Shav-Tal Y. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLOS Biology 2011; 9:e1000573; PMID:21264352
   PubMed Web of Science ®Google Scholar
• Davidson PM, Lammerding J. Broken nuclei – lamins, nuclear mechanics, and disease. Trends Cell Biol 2013; 24:247-56; PMID:24309562; http://dx.doi.org/10.1016/j.tcb.2013.11.004
   PubMed Web of Science ®Google Scholar
• Gonzalez-Suarez I, Redwood AB, Perkins SM, Vermolen B, Lichtensztejin D, Grotsky DA, Morgado-Palacin L, Gapud EJ, Sleckman BP, Sullivan T, et al. Novel roles for A-type lamins in telomere biology and the DNA damage response pathway. EMBO J 2009; 28:2414-27; PMID:19629036; http://dx.doi.org/10.1038/emboj.2009.196
   PubMed Web of Science ®Google Scholar
• Leonardi E, Girlando S, Serio G, Mauri FA, Perrone G, Scampini S, Dalla Palma P, Barbareschi M. PCNA and Ki67 expression in breast carcinoma: Correlations with clinical and biological variables. J Clin Pathol 1992; 45:416-9; PMID:1350788; http://dx.doi.org/10.1136/jcp.45.5.416
   PubMed Web of Science ®Google Scholar
• Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, Kashiwagi S, Fukami K, Miyata T, Miyoshi H. Visualizing spatiotemporal dynamics of multicellular cell-cycle -progression. Cell 2008; 132:487-98; PMID:18267078; http://dx.doi.org/10.1016/j.cell.2007.12.033
   PubMed Web of Science ®Google Scholar
• Platani M, Goldberg I, Lamond AI, Swedlow JR. Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 2002; 4:502-8; PMID:12068306; http://dx.doi.org/10.1038/ncb809
   PubMed Web of Science ®Google Scholar
• Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL, Singer RH. Dynamics of single mRNPs in nuclei of living cells. Science 2004; 304:1797-800; PMID:15205532; http://dx.doi.org/10.1126/science.1099754
   PubMed Web of Science ®Google Scholar
• Görisch SM, Wachsmuth M, Ittrich C, Bacher CP, Rippe K, Lichter P. Nuclear body movement is determined by chromatin accessibility and dynamics. Proc Natl Acad Sci USA 2004; 101:13221-6; PMID:15331777; http://dx.doi.org/10.1073/pnas.0402958101
   PubMed Web of Science ®Google Scholar
• Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol 2010; 12:543-52; PMID:20453848; http://dx.doi.org/10.1038/ncb2056
   PubMed Web of Science ®Google Scholar
• Kolin DL, Wiseman PW. Advances in image correlation spectroscopy: Measuring number densities, aggregation states, and dynamics of fluorescently labeled macromolecules in cells. Cell Biochem Biophys 2007; 49:141-64; PMID:17952641; http://dx.doi.org/10.1007/s12013-007-9000-5
   PubMed Web of Science ®Google Scholar
• Llères D, James J, Swift S, Norman DG, Lamond AI. Quantitative analysis of chromatin compaction in living cells using FLIM–FRET. J Cell Biol 2009; 187:481-96; http://dx.doi.org/10.1083/jcb.200907029
   PubMed Web of Science ®Google Scholar