Genomes and Genes
Summary: The mechanisms of eukaryotic CELLS that place or keep the CHROMOSOMES in a particular SUBNUCLEAR SPACE.
- Porter I, McClelland S, Khoudoli G, Hunter C, Andersen J, McAinsh A, et al. Bod1, a novel kinetochore protein required for chromosome biorientation. J Cell Biol. 2007;179:187-97 pubmed..Therefore, Bod1 is a novel kinetochore protein that is required for the detection or resolution of syntelic attachments in mitotic spindles. ..
- Meaburn K, Misteli T. Cell biology: chromosome territories. Nature. 2007;445:379-781 pubmed
- Iyer K, Maharana S, Gupta S, Libchaber A, Tlusty T, Shivashankar G. Modeling and experimental methods to probe the link between global transcription and spatial organization of chromosomes. PLoS ONE. 2012;7:e46628 pubmed publisher..Taken together, our methods highlight the functional coupling between topology of chromosomes and their respective gene expression patterns...
- Branco M, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol. 2006;4:e138 pubmed..These findings suggest that local chromatin conformation and gene transcription influence the extent with which chromosomes interact and affect their overall properties, with direct consequences for cell-type specific genome stability. ..
- Kuroda M, Tanabe H, Yoshida K, Oikawa K, Saito A, Kiyuna T, et al. Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci. 2004;117:5897-903 pubmed..translocation of chromosomes 12 and 16, our observations indicate that alteration of relative chromosome positioning might play a key role in the tumorigenesis of human liposarcomas...
- Spilianakis C, Lalioti M, Town T, Lee G, Flavell R. Interchromosomal associations between alternatively expressed loci. Nature. 2005;435:637-45 pubmed..Thus, we provide an example of eukaryotic genes located on separate chromosomes associating physically in the nucleus via interactions that may have a function in coordinating gene expression. ..
- Strickfaden H, Zunhammer A, van Koningsbruggen S, Köhler D, Cremer T. 4D chromatin dynamics in cycling cells: Theodor Boveri's hypotheses revisited. Nucleus. 2010;1:284-97 pubmed publisher..A new model of chromatin dynamics is proposed. It suggests that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements. ..
- Kwon M, Morales Mulia S, Brust Mascher I, Rogers G, Sharp D, Scholey J. The chromokinesin, KLP3A, dives mitotic spindle pole separation during prometaphase and anaphase and facilitates chromatid motility. Mol Biol Cell. 2004;15:219-33 pubmed..We propose that KLP3A acts on MTs associated with chromosome arms and the central spindle to organize ipMT bundles, to drive spindle pole separation and to facilitate chromatid motility. ..
- Weaver L, Ems McClung S, Stout J, Leblanc C, Shaw S, Gardner M, et al. Kif18A uses a microtubule binding site in the tail for plus-end localization and spindle length regulation. Curr Biol. 2011;21:1500-6 pubmed publisher..Members of the kinesin-8 family are important for the regulation of spindle length and for chromosome positioning [2-9]...
- Stumpff J, Von Dassow G, Wagenbach M, Asbury C, Wordeman L. The kinesin-8 motor Kif18A suppresses kinetochore movements to control mitotic chromosome alignment. Dev Cell. 2008;14:252-62 pubmed publisher..Based on these findings, we propose a molecular model in which Kif18A regulates kinetochore microtubule dynamics to control mitotic chromosome positioning.
- Foster H, Griffin D, Bridger J. Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues. BMC Cell Biol. 2012;13:30 pubmed publisher..In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome ..
- Misteli T. Spatial positioning; a new dimension in genome function. Cell. 2004;119:153-6 pubmed..Recent observations have highlighted the important yet still largely mysterious role of spatial positioning in genome activity and stability. ..
- Heride C, Ricoul M, Kiêu K, von Hase J, Guillemot V, Cremer C, et al. Distance between homologous chromosomes results from chromosome positioning constraints. J Cell Sci. 2010;123:4063-75 pubmed publisher..Maintaining distance between homologous chromosomes in human cells could participate in regulating genome stability and gene expression, both mechanisms that are key players in tumorigenesis. ..
- Gehlen L, Gruenert G, Jones M, Rodley C, Langowski J, O Sullivan J. Chromosome positioning and the clustering of functionally related loci in yeast is driven by chromosomal interactions. Nucleus. 2012;3:370-83 pubmed..Our results support a link between structure and transcription that occurs within the context of a flexible genome organization. ..
- Kosak S, Scalzo D, Alworth S, Li F, Palmer S, Enver T, et al. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol. 2007;5:e309 pubmed..We suggest that proximity in the form of chromosomal gene distribution and homolog association may be the basis for organizing the genome for coordinate gene regulation during cellular differentiation. ..
- Meaburn K, Levy N, Toniolo D, Bridger J. Chromosome positioning is largely unaffected in lymphoblastoid cell lines containing emerin or A-type lamin mutations. Biochem Soc Trans. 2005;33:1438-40 pubmed..Despite highly aberrant nuclear distributions of A-type lamins and emerin in lymphoblastoid cell lines derived from patients with emerin or lamin A mutations, little or no change in chromosome location was detected. ..
- Fraser P, Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature. 2007;447:413-7 pubmed..A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it...
- Stumpff J, Wagenbach M, Franck A, Asbury C, Wordeman L. Kif18A and chromokinesins confine centromere movements via microtubule growth suppression and spatial control of kinetochore tension. Dev Cell. 2012;22:1017-29 pubmed publisher..These data support a model in which Kif18A and polar ejection forces synergistically promote centromere alignment via spatial control of kinetochore-microtubule dynamics. ..
- Guelen L, Pagie L, Brasset E, Meuleman W, Faza M, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008;453:948-51 pubmed publisher..Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus...
- Ganai N, Sengupta S, Menon G. Chromosome positioning from activity-based segregation. Nucleic Acids Res. 2014;42:4145-59 pubmed publisher..Results from our model are in reasonable agreement with experimental data and we make a number of predictions that can be tested in experiments. ..
- Royo F, Paz N, Espinosa L, McQueen P, VellÃ³n L, Parada L. Spatial link between nucleoli and expression of the Zac1 gene. Chromosoma. 2009;118:711-22 pubmed publisher..Our data demonstrate that Zac1 mRNA preferentially accumulates in close proximity to nucleoli within the cell nucleus. In addition, our results suggest a functional link between such spatial distribution and protein expression. ..
- Greaves I, Rens W, Ferguson Smith M, Griffin D, Marshall Graves J. Conservation of chromosome arrangement and position of the X in mammalian sperm suggests functional significance. Chromosome Res. 2003;11:503-12 pubmed
- Paschal C, Maciejowski J, Jallepalli P. A stringent requirement for Plk1 T210 phosphorylation during K-fiber assembly and chromosome congression. Chromosoma. 2012;121:565-72 pubmed publisher..Collectively, our data indicate that K-fibers are sensitive to even subtle perturbations in T210 phosphorylation and caution against relying on Plk1(T210D) as an in vivo surrogate for the natively activated kinase. ..
- McEwen B, Dong Y, VandenBeldt K. Using electron microscopy to understand functional mechanisms of chromosome alignment on the mitotic spindle. Methods Cell Biol. 2007;79:259-93 pubmed
- Ali A, Veeranki S, Chinchole A, Tyagi S. MLL/WDR5 Complex Regulates Kif2A Localization to Ensure Chromosome Congression and Proper Spindle Assembly during Mitosis. Dev Cell. 2017;41:605-622.e7 pubmed publisher..Our findings highlight a non-canonical mitotic function of MLL complex, which may have a direct impact on chromosomal stability, frequently compromised in cancer. ..
- Razin S, Petrov A, Hair A, Vassetzky Y. Chromatin domains and territories: flexibly rigid. Crit Rev Eukaryot Gene Expr. 2004;14:79-88 pubmed..The present review discusses the implications of the organization of chromosomal domains and territories in development and carcinogenesis. ..
- Pattenden S, Chandy M, Gutiérrez J, Workman J. Chromatin dynamics rule the genome. Genome Biol. 2005;6:355 pubmed
- Howard M. Cell division: experiments and modelling unite to resolve the middle. Curr Biol. 2009;19:R67-9 pubmed publisher..Quantitative modelling has now further scrutinised these ideas, yielding fresh insights into furrow positioning. ..
- Ohyama T. [Genetic information carried in DNA conformation and physical properties]. Tanpakushitsu Kakusan Koso. 2008;53:1-11 pubmed
- Pliss A, Malyavantham K, Bhattacharya S, Zeitz M, Berezney R. Chromatin dynamics is correlated with replication timing. Chromosoma. 2009;118:459-70 pubmed publisher..Analysis of ChrD colocalization with transcription sites and cDNA with ChrD and transcription sites further supports this proposal. ..
- Gradolatto A, Smart S, Byrum S, Blair L, Rogers R, Kolar E, et al. A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. Mol Cell Biol. 2009;29:4604-11 pubmed publisher..This work demonstrates that the Yta7 bromodomain engages histones for certain cellular functions like barrier chromatin maintenance and particular Spt16/Asf1 cellular pathways of chromatin regulation. ..
- O Sullivan J. Chromosome organizaton in simple and complex unicellular organisms. Curr Issues Mol Biol. 2011;13:37-42 pubmed..g. episomes) present within complex genomes. In this comment, I will highlight similarities in the spatial organization of eukaryotic and prokaryotic unicellular genomes. ..
- Mehta I, Kulashreshtha M, Chakraborty S, Kolthur Seetharam U, Rao B. Chromosome territories reposition during DNA damage-repair response. Genome Biol. 2013;14:R135 pubmed publisher..Thus, our report for the first time highlights DNA damage-dependent spatial reorganization of whole chromosomes, which might be an integral aspect of cellular damage response. ..
- O Sullivan J, Sontam D, Grierson R, Jones B. Repeated elements coordinate the spatial organization of the yeast genome. Yeast. 2009;26:125-38 pubmed publisher..These data establish a dynamic domain model for yeast genome organization. Moreover, they point to the repeated elements playing a central role in the dynamic organization of genome architecture. ..
- Mehta I, Elcock L, Amira M, Kill I, Bridger J. Nuclear motors and nuclear structures containing A-type lamins and emerin: is there a functional link?. Biochem Soc Trans. 2008;36:1384-8 pubmed publisher..If any of the components are lacking or aberrant, then the nuclear motor complex involved in moving chromosomes or genes will be dysfunctional, leading to an inability to move chromosomes in response to signalling events. ..
- Malyavantham K, Bhattacharya S, Alonso W, Acharya R, Berezney R. Spatio-temporal dynamics of replication and transcription sites in the mammalian cell nucleus. Chromosoma. 2008;117:553-67 pubmed publisher..Our results further suggest that the early RS chromatin domains are transcribing genes throughout the cell cycle and that multiple chromatin domains are organized around the same transcription factory. ..
- Taimen P, Pfleghaar K, Shimi T, Möller D, Ben Harush K, Erdos M, et al. A progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization. Proc Natl Acad Sci U S A. 2009;106:20788-93 pubmed publisher..The study also emphasizes the importance of lamins in nuclear assembly and chromatin organization. ..
- Santos M, Zintzaras E, Szathmary E. Recombination in primeval genomes: a step forward but still a long leap from maintaining a sizable genome. J Mol Evol. 2004;59:507-19 pubmed..However, the upper bound of informational length would still be far from the "minimal life" provisions. ..
- Tirosh I, Sigal N, Barkai N. Widespread remodeling of mid-coding sequence nucleosomes by Isw1. Genome Biol. 2010;11:R49 pubmed publisher..The differential specificity of the two remodelers may be specified through interactions with particular histone marks. ..
- Goodyer W, Kaitna S, Couteau F, Ward J, Boulton S, Zetka M. HTP-3 links DSB formation with homolog pairing and crossing over during C. elegans meiosis. Dev Cell. 2008;14:263-74 pubmed publisher..Our study reveals a mechanism for coupling meiotic DSB formation with homolog pairing through the essential participation of an axis component with complexes mediating both processes. ..
- Zeitz M, Mukherjee L, Bhattacharya S, Xu J, Berezney R. A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts. J Cell Physiol. 2009;221:120-9 pubmed publisher..We conclude that a large subset of human chromosomes has a preferred probabilistic arrangement in WI38 cells and that the resulting chromosomal associations show tissue origin specificity. ..
- Mo X, Feng Z, Hu W. [Application and progress of fluorescence in situ hybridization in schistosome biology]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi. 2011;29:224-8, 232 pubmed..This article reviews the application of FISH in schistosome biology and its potential development. ..
- Snyder J, Ha Y, Olsofka C, Wahdan R. Both actin and myosin inhibitors affect spindle architecture in PtK1 cells: does an actomyosin system contribute to mitotic spindle forces by regulating attachment and movements of chromosomes in mammalian cells?. Protoplasma. 2010;240:57-68 pubmed publisher..Evidence is presented to suggest that an actomyosin system may help to regulate the initial and continued attachment of chromosomes to the mammalian spindle and could also influence spindle checkpoint(s)...
- Peric Hupkes D, Meuleman W, Pagie L, Bruggeman S, Solovei I, Brugman W, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010;38:603-13 pubmed publisher..These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. ..
- Boei J, Fomina J, Darroudi F, Nagelkerke N, Mullenders L. Interphase chromosome positioning affects the spectrum of radiation-induced chromosomal aberrations. Radiat Res. 2006;166:319-26 pubmed..Here we show that the spectrum of interchanges deviates significantly from one expected based on random chromosome positioning. Moreover, the observed exchange interactions between specific chromosome pairs as well as the ..
- Namekawa S, Park P, Zhang L, Shima J, McCarrey J, Griswold M, et al. Postmeiotic sex chromatin in the male germline of mice. Curr Biol. 2006;16:660-7 pubmed..We conclude that chromosome-wide X silencing continues from meiosis to the end of spermiogenesis, and we discuss implications for proposed mechanisms of imprinted X-inactivation. ..
- Kops G. Dividing the goods: co-ordination of chromosome biorientation and mitotic checkpoint signalling by mitotic kinases. Biochem Soc Trans. 2009;37:971-5 pubmed publisher..A group of unrelated kinases controls various aspects of both processes. The present short review outlines our current understanding of the roles of these kinases in maintaining chromosomal stability. ..
- Figueroa R, Gudise S, Larsson V, Hallberg E. A transmembrane inner nuclear membrane protein in the mitotic spindle. Nucleus. 2010;1:249-53 pubmed publisher..Hence, the protein was named Samp1, Spindle associated membrane protein 1. Secondly, it displays a functional connection to centrosomes. This article discusses various aspects of Samp1 in relation to possible cellular function(s). ..
- Tsankov A, Thompson D, Socha A, Regev A, Rando O. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 2010;8:e1000414 pubmed publisher..Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation. ..