The spatial repositioning of adipogenesis genes is correlated with their expression status in a porcine mesenchymal stem cell adipogenesis model system (original) (raw)
References
Anderson SI, Lopez-Corrales NL, Gorick B, Archibald AL (2000) A large-fragment porcine genomie library resource in a BAC vector. Mamm Genome 9:811–814 Article Google Scholar
Ballabio E, Cantarella CD, Federico C, Di Mare P, Hall G, Harbott J, Hughes J, Saccone S, Tosi S (2009) Ectopic expression of the HLXB9 gene is associated with an altered nuclear position in t(7;12) leukaemias. Leukemia 23(6):1179–1182 ArticlePubMedCAS Google Scholar
Bártová E, Kozubek S, Jirsová P, Kozubek M, Gajová H, Lukásová E, Skalníková M, Ganová A, Koutná I, Hausmann M (2002) Nuclear structure and gene activity in human differentiated cells. J Struct Biol 139:76–89 ArticlePubMedCAS Google Scholar
Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA (2001) The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10:211–219 ArticlePubMedCAS Google Scholar
Brown KE, Baxter J, Graf D, Merkenschlager M, Fisher AG (1999) Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol Cell 3:207–217 ArticlePubMedCAS Google Scholar
Brown KE, Amoils S, Horn JM, Buckle VJ, Higgs DR, Merkenschlager M, Fisher AG (2001) Expression of alpha- and beta-globin genes occurs within different nuclear domains in haemopoietic cells. Nat Cell Biol 3:602–606 ArticlePubMedCAS Google Scholar
Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172:177–187 ArticlePubMedCAS Google Scholar
Brown JM, Green J, das Neves RP, Wallace HA, Smith AJ, Hughes J, Gray N, Taylor S, Wood WG, Higgs DR, Iborra FJ, Buckle VJ (2008) Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182:1083–1097 ArticlePubMedCAS Google Scholar
Bridger JM, Herrmann H, Muenkel C, Lichter P (1998) Identification of an interchromosomal compartment by polymerisation of nuclear-targeted vimentin. J Cell Sci 111:1241–1253 PubMedCAS Google Scholar
Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119–1130 ArticlePubMedCAS Google Scholar
Chambeyron S, Da Silva NR, Lawson KA, Bickmore WA (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132:2215–2223 ArticlePubMedCAS Google Scholar
Chen K, Baxter T, Muir WM, Groenen MA, Schook LB (2007) Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci 3:153–165 ArticlePubMed Google Scholar
Chubb JR, Bickmore WA (2003) Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112:403–406 ArticlePubMedCAS Google Scholar
Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S (2006) Chromosome territories—a functional nuclear landscape. Curr Opin Cell Biol 18:307–316 ArticlePubMedCAS Google Scholar
Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA (1999) Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145:1119–1131 ArticlePubMedCAS Google Scholar
Ehlers JP, Worley L, Onken MD, Harbour JW (2005) DDEF1 is located in an amplified region of chromosome 8q and is overexpressed in uveal melanoma. Clin Cancer Res 11:3609–3613 ArticlePubMedCAS Google Scholar
Federico C, Cantarella CD, Di Mare P, Tosi S, Saccone S (2008) The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density. Chromosoma 117:399–410 ArticlePubMedCAS Google Scholar
Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA (2008) Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4:e1000039 ArticlePubMedCAS Google Scholar
Formiguera X, Cantón A (2004) Obesity: epidemiology and clinical aspects. Best Pract Res Clin Gastroenterol 18:1125–1146 PubMed Google Scholar
Foster HA, Bridger JM (2005) The genome and the nucleus: a marriage made by evolution. Genome organisation and nuclear architecture. Chromosoma 114:212–229 ArticlePubMed Google Scholar
Foster HA, Abeydeera LR, Griffin DK, Bridger JM (2005) Non-random chromosome positioning in mammalian sperm nuclei, with migration of the sex chromosomes during late spermatogenesis. J Cell Sci 118:1811–1820 ArticlePubMedCAS Google Scholar
Goetze S, Mateos-Langerak J, Gierman HJ, de Leeuw W, Giromus O, Indemans MH, Koster J, Ondrej V, Versteeg R, van Driel R (2007) The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol Cell Biol 27:4475–4487 ArticlePubMedCAS Google Scholar
Grasser F, Neusser M, Fiegler H, Thormeyer T, Cremer M, Carter NP, Cremer T, Müller S (2008) Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei. J Cell Sci 121:1876–1886 ArticlePubMedCAS Google Scholar
Guo X, Liao K (2000) Analysis of gene expression profile during 3T3-L1 preadipocyte differentiation. Gene 251:45–53 ArticlePubMedCAS Google Scholar
Habermann FA, Cremer M, Walter J, Kreth G, von Hase J, Bauer K, Wienberg J, Cremer C, Cremer T, Solovei I (2001) Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res 9:569–584 ArticlePubMedCAS Google Scholar
Hofmann WA, Johnson T, Klapczynski M, Fan JL, de Lanerolle P (2006) From transcription to transport: emerging roles for nuclear myosin I. Biochem Cell Biol 84:418–426 ArticlePubMedCAS Google Scholar
Hu Q, Kwon YS, Nunez E, Cardamone MD, Hutt KR, Ohgi KA, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MG, Fu XD (2008) Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc Natl Acad Sci U S A 105:19199–19204 ArticlePubMedCAS Google Scholar
Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, Singh H (2002) Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296:158–162 ArticlePubMedCAS Google Scholar
Kouadjo KE, Nishida Y, Cadrin-Girard JF, Yoshioka M, St-Amand J (2007) Housekeeping and tissue-specific genes in mouse tissues. BMC Genomics 8:127 ArticlePubMedCAS Google Scholar
Küpper K, Kölbl A, Biener D, Dittrich S, von Hase J, Thormeyer T, Fiegler H, Carter NP, Speicher MR, Cremer T, Cremer M (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116:285–306 ArticlePubMed Google Scholar
Kuroda M, Tanabe H, Yoshida K, Oikawa K, Saito A, Kiyuna T, Mizusawa H, Mukai K (2004) Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci 117:5897–5903 ArticlePubMedCAS Google Scholar
Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T (2007) Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 8:104–115 ArticlePubMedCAS Google Scholar
Lunney JK (2007) Advances in swine biomedical model genomics. Int J Biol Sci 3:179–184 PubMedCAS Google Scholar
Meaburn KJ, Misteli T (2008) Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol 180:39–50 ArticlePubMedCAS Google Scholar
Meaburn KJ, Cabuy E, Bonne G, Levy N, Morris GE, Novelli G, Kill IR, Bridger JM (2007) Primary laminopathy fibroblasts display altered genome organization and apoptosis. Aging Cell 6:139–153 ArticlePubMedCAS Google Scholar
Mehta IS, Elcock LS, Amira M, Kill IR, Bridger JM (2008) Nuclear motors and nuclear structures containing A-type lamins and emerin: is there a functional link? Biochem Soc Trans 36:1384–1388 ArticlePubMedCAS Google Scholar
Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128:787–800 ArticlePubMedCAS Google Scholar
Morey C, Da Silva NR, Perry P, Bickmore WA (2007) Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 134:909–919 ArticlePubMedCAS Google Scholar
Morey C, Kress C, Bickmore WA (2009) Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to upregulate gene expression. Genome Res (in press)
Nakamura T, Shiojima S, Hirai Y, Iwama T, Tsuruzoe N, Hirasawa A, Katsuma S, Tsujimoto G (2003) Temporal gene expression changes during adipogenesis in human mesenchymal stem cells. Biochem Biophys Res Commun 303:306–312 ArticlePubMedCAS Google Scholar
Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36:1065–1071 ArticlePubMedCAS Google Scholar
Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P (2007) Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 5:e192 ArticlePubMedCAS Google Scholar
Pérez-Mancera PA, Bermejo-Rodríguez C, González-Herrero I, Herranz M, Flores T, Jiménez R, Sánchez-García I (2007) Adipose tissue mass is modulated by SLUG (SNAI2). Hum Mol Genet 16:2972–2986 ArticlePubMedCAS Google Scholar
Ragoczy T, Bender MA, Telling A, Byron R, Groudine M (2006) The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 20:1447–1457 ArticlePubMedCAS Google Scholar
Reddy KL, Zullo JM, Bertolino E, Singh H (2008) Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452:243–247 ArticlePubMedCAS Google Scholar
Rosen ED, MacDougald OA (2006) Adipocyte differentiation from the inside out. Nat Rev Mol Cell Biol 7:885–896 ArticlePubMedCAS Google Scholar
Saccone S, Federico C, Bernardi G (2002) Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene 300:169–178 ArticlePubMedCAS Google Scholar
Sadoni N, Targosz BS, Englmann A, Fesser S, Koch J, Schindelhauer D, Zink D (2008) Transcription-dependent spatial arrangements of CFTR and conserved adjacent loci are not conserved in human and murine nuclei. Chromosoma 117:381–397 ArticlePubMedCAS Google Scholar
Schöfer C, Weipoltshammer K (2008) Gene dynamics and nuclear architecture during differentiation. Differentiation 76:41–56 PubMed Google Scholar
Schook L, Beattie C, Beever J, Donovan S, Jamison R, Zuckermann F, Niemi S, Rothschild M, Rutherford M, Smith D (2005) Swine in biomedical research: creating the building blocks of animal models. Anim Biotechnol 16:183–190 ArticlePubMed Google Scholar
Somech R, Shaklai S, Geller O, Amariglio N, Simon AJ, Rechavi G, Gal-Yam EN (2005) The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation. J Cell Sci 118:4017–4025 ArticlePubMedCAS Google Scholar
Szczerbal I, Chmurzynska A (2008) Chromosomal localization of nine porcine genes encoding transcription factors involved in adipogenesis. Cytogenet Genome Res 121:50–54 ArticlePubMedCAS Google Scholar
Szczerbal I, Chmurzynska A, Switonski M (2007a) Cytogenetic mapping of eight genes encoding fatty acid binding proteins (FABPs) in the pig genome. Cytogenet Genome Res 118:63–66 ArticlePubMedCAS Google Scholar
Szczerbal I, Lin L, Stachowiak M, Chmurzynska A, Mackowski M, Winter A, Flisikowski K, Fries R, Switonski M (2007b) Cytogenetic mapping of DGAT1, PPARA, ADIPOR1 and CREB genes in the pig. J Appl Genet 48:73–76 PubMed Google Scholar
Takizawa T, Gudla PR, Guo L, Lockett S, Misteli T (2008a) Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev 22:489–498 ArticlePubMedCAS Google Scholar
Tanabe H, Habermann FA, Solovei I, Cremer M, Cremer T (2002a) Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutat Res 504:37–45 PubMedCAS Google Scholar
Tanabe H, Müller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T (2002b) Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A 99:4424–4429 ArticlePubMedCAS Google Scholar
Tong Q, Dalgin G, Xu H, Ting CN, Leiden JM, Hotamisligil GS (2000) Function of GATA transcription factors in preadipocyte–adipocyte transition. Science 290:134–138 ArticlePubMedCAS Google Scholar
Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D (2000) Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113:1565–1576 PubMedCAS Google Scholar
Williams RR, Broad S, Sheer D, Ragoussis J (2002) Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp Cell Res 272:163–175 ArticlePubMedCAS Google Scholar
Williams RR, Azuara V, Perry P, Sauer S, Dvorkina M, Jørgensen H, Roix J, McQueen P, Misteli T, Merkenschlager M, Fisher AG (2006) Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci 119:132–140 ArticlePubMedCAS Google Scholar
Xu M, Cook PR (2008) The role of specialized transcription factories in chromosome pairing. Biochim Biophys Acta 1783:2155–2160 ArticlePubMedCAS Google Scholar
Zalenskaya IA, Zalensky AO (2004) Non-random positioning of chromosomes in human sperm nuclei. Chromosome Res 12:163–173 ArticlePubMedCAS Google Scholar
Zeng L, Rahrmann E, Hu Q, Lund T, Sandquist L, Felten M, O'Brien TD, Zhang J, Verfaillie C (2006) Multipotent adult progenitor cells from swine bone marrow. Stem Cells 24:2355–2366 ArticlePubMedCAS Google Scholar
Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, Rudolph C, Alt F, Luther K, Braz C, Sadoni N, Rosenecker J, Schindelhauer D (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166:815–825 ArticlePubMedCAS Google Scholar
Zou L, Zou X, Chen L, Li H, Mygind T, Kassem M, Bünger C (2008) Multilineage differentiation of porcine bone marrow stromal cells associated with specific gene expression pattern. J Orthop Res 26:56–64 ArticlePubMedCAS Google Scholar