Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories
10.1007/s00018-013-1465-3
Crossref journal-article
Springer Science and Business Media LLC
Cellular and Molecular Life Sciences (297)
Bibliography

Rieder, D., Ploner, C., Krogsdam, A. M., Stocker, G., Fischer, M., Scheideler, M., Dani, C., Amri, E.-Z., Müller, W. G., McNally, J. G., & Trajanoski, Z. (2013). Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories. Cellular and Molecular Life Sciences, 71(9), 1741–1759.

Authors 11
  1. Dietmar Rieder (first)
  2. Christian Ploner (additional)
  3. Anne M. Krogsdam (additional)
  4. Gernot Stocker (additional)
  5. Maria Fischer (additional)
  6. Marcel Scheideler (additional)
  7. Christian Dani (additional)
  8. Ez-Zoubir Amri (additional)
  9. Waltraud G. Müller (additional)
  10. James G. McNally (additional)
  11. Zlatko Trajanoski (additional)
References 69 Referenced 40
  1. Osborne CS, Chakalova L, Brown KE et al (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36:1065–1071 (10.1038/ng1423) / Nat Genet by CS Osborne (2004)
  2. 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 (10.1083/jcb.200507073) / J Cell Biol by JM Brown (2006)
  3. Brown JM, Green J, das Neves RP et al (2008) Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182:1083–1097 (10.1083/jcb.200803174) / J Cell Biol by JM Brown (2008)
  4. Schoenfelder S, Sexton T, Chakalova L et al (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42:53–61 (10.1038/ng.496) / Nat Genet by S Schoenfelder (2010)
  5. Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26:183–186 (10.1038/79896) / Nat Genet by BA Cohen (2000)
  6. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418:975–979 (10.1038/nature01012) / Nature by PJ Roy (2002)
  7. Kosak ST, Scalzo D, Alworth SV, Li F, Palmer S, Enver T, Lee JSJ, Groudine M (2007) Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 5:e309 (10.1371/journal.pbio.0050309) / PLoS Biol by ST Kosak (2007)
  8. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420:666–669 (10.1038/nature01216) / Nature by AM Boutanaev (2002)
  9. Mezey J, Nuzhdin S, Ye F, Jones C (2008) Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol 8:2 (10.1186/1471-2148-8-2) / BMC Evol Biol by J Mezey (2008)
  10. Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, Hayashizaki Y, Huber W, Sperling S (2007) Genomic organization of transcriptomes in mammals: coregulation and cofunctionality. Genomics 89:580–587 (10.1016/j.ygeno.2007.01.010) / Genomics by A Purmann (2007)
  11. Vogel JH, von Heydebreck A, Purmann A, Sperling S (2005) Chromosomal clustering of a human transcriptome reveals regulatory background. BMC Bioinformatics 6:230 (10.1186/1471-2105-6-230) / BMC Bioinformatics by JH Vogel (2005)
  12. Nora EP, Lajoie BR, Schulz EG et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485:381–385 (10.1038/nature11049) / Nature by EP Nora (2012)
  13. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376–380 (10.1038/nature11082) / Nature by JR Dixon (2012)
  14. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148:458–472 (10.1016/j.cell.2012.01.010) / Cell by T Sexton (2012)
  15. 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 (10.1371/journal.pbio.0050192) / PLoS Biol by CS Osborne (2007)
  16. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA (2005) Interchromosomal associations between alternatively expressed loci. Nature 435:637–645 (10.1038/nature03574) / Nature by CG Spilianakis (2005)
  17. Takizawa T, Gudla PR, Guo L, Lockett S, Misteli T (2008) Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes Dev 22:489–498 (10.1101/gad.1634608) / Genes Dev by T Takizawa (2008)
  18. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38:1348–1354 (10.1038/ng1896) / Nat Genet by M Simonis (2006)
  19. Palstra R-J, Simonis M, Klous P, Brasset E, Eijkelkamp B, de Laat W (2008) Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One 3:e1661 (10.1371/journal.pone.0001661) / PLoS One by R-J Palstra (2008)
  20. Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64 (10.1038/nature08497) / Nature by MJ Fullwood (2009)
  21. Li G, Ruan X, Auerbach RK et al (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148:84–98 (10.1016/j.cell.2011.12.014) / Cell by G Li (2012)
  22. Shopland LS, Johnson CV, Byron M, McNeil J, Lawrence JB (2003) Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J Cell Biol 162:981–990 (10.1083/jcb.200303131) / J Cell Biol by LS Shopland (2003)
  23. Szczerbal I, Bridger JM (2010) Association of adipogenic genes with SC-35 domains during porcine adipogenesis. Chromosome Res 18:887–895 (10.1007/s10577-010-9176-1) / Chromosome Res by I Szczerbal (2010)
  24. Cook PR (1999) The organization of replication and transcription. Science 284:1790–1795 (10.1126/science.284.5421.1790) / Science by PR Cook (1999)
  25. Iborra FJ, Pombo A, Jackson DA, Cook PR (1996) Active RNA polymerases are localized within discrete transcription “factories” in human nuclei. J Cell Sci 109(Pt 6):1427–1436 (10.1242/jcs.109.6.1427) / J Cell Sci by FJ Iborra (1996)
  26. Iborra FJ, Pombo A, McManus J, Jackson DA, Cook PR (1996) The topology of transcription by immobilized polymerases. Exp Cell Res 229:167–173 (10.1006/excr.1996.0355) / Exp Cell Res by FJ Iborra (1996)
  27. Papantonis A, Larkin JD, Wada Y, Ohta Y, Ihara S, Kodama T, Cook PR (2010) Active RNA polymerases: mobile or immobile molecular machines? PLoS Biol 8:e1000419 (10.1371/journal.pbio.1000419) / PLoS Biol by A Papantonis (2010)
  28. Rieder D, Trajanoski Z, McNally JG (2012) Transcription factories. Front Genet 3:221 (10.3389/fgene.2012.00221) / Front Genet by D Rieder (2012)
  29. Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, Fischer C, Solovei I, Cremer C, Cremer T (2001) Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res 9:541–567 (10.1023/A:1012495201697) / Chromosome Res by M Cremer (2001)
  30. Parada LA, McQueen PG, Munson PJ, Misteli T (2002) Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol 12:1692–1697 (10.1016/S0960-9822(02)01166-1) / Curr Biol by LA Parada (2002)
  31. Meaburn KJ, Misteli T (2008) Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol 180:39–50 (10.1083/jcb.200708204) / J Cell Biol by KJ Meaburn (2008)
  32. Rajapakse I, Perlman MD, Scalzo D, Kooperberg C, Groudine M, Kosak ST (2009) The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc Natl Acad Sci USA 106:6679–6684 (10.1073/pnas.0900986106) / Proc Natl Acad Sci USA by I Rajapakse (2009)
  33. Rodriguez A-M, Pisani D, Dechesne CA et al (2005) Transplantation of a multipotent cell population from human adipose tissue induces dystrophin expression in the immunocompetent mdx mouse. J Exp Med 201:1397–1405 (10.1084/jem.20042224) / J Exp Med by A-M Rodriguez (2005)
  34. Scheideler M, Elabd C, Zaragosi L-E et al (2008) Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. BMC Genomics 9:340 (10.1186/1471-2164-9-340) / BMC Genomics by M Scheideler (2008)
  35. Lamond AI, Spector DL (2003) Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4:605–612 (10.1038/nrm1172) / Nat Rev Mol Cell Biol by AI Lamond (2003)
  36. Bond CS, Fox AH (2009) Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol 186:637–644 (10.1083/jcb.200906113) / J Cell Biol by CS Bond (2009)
  37. Ching RW, Dellaire G, Eskiw CH, Bazett-Jones DP (2005) PML bodies: a meeting place for genomic loci? J Cell Sci 118:847–854 (10.1242/jcs.01700) / J Cell Sci by RW Ching (2005)
  38. Dundr M, Misteli T (2010) Biogenesis of nuclear bodies. Cold Spring Harb Perspect Biol 2:a000711 (10.1101/cshperspect.a000711) / Cold Spring Harb Perspect Biol by M Dundr (2010)
  39. Chodosh LA, Fire A, Samuels M, Sharp PA (1989) 5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole inhibits transcription elongation by RNA polymerase II in vitro. J Biol Chem 264:2250–2257 (10.1016/S0021-9258(18)94169-4) / J Biol Chem by LA Chodosh (1989)
  40. Marshall NF, Price DH (1992) Control of formation of two distinct classes of RNA polymerase II elongation complexes. Mol Cell Biol 12:2078–2090 (10.1128/MCB.12.5.2078) / Mol Cell Biol by NF Marshall (1992)
  41. Bensaude O (2011) Inhibiting eukaryotic transcription: which compound to choose? How to evaluate its activity? Transcription 2:103–108 (10.4161/trns.2.3.16172) / Transcription by O Bensaude (2011)
  42. Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol 4:e138 (10.1371/journal.pbio.0040138) / PLoS Biol by MR Branco (2006)
  43. Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293 (10.1126/science.1181369) / Science by E Lieberman-Aiden (2009)
  44. Olivares-Chauvet P, Fennessy D, Jackson DA, Maya-Mendoza A (2011) Innate structure of DNA foci restricts the mixing of DNA from different chromosome territories. PLoS One 6:e27527 (10.1371/journal.pone.0027527) / PLoS One by P Olivares-Chauvet (2011)
  45. Duncan PI, Stojdl DF, Marius RM, Scheit KH, Bell JC (1998) The Clk2 and Clk3 dual-specificity protein kinases regulate the intranuclear distribution of SR proteins and influence pre-mRNA splicing. Exp Cell Res 241:300–308 (10.1006/excr.1998.4083) / Exp Cell Res by PI Duncan (1998)
  46. Sacco-Bubulya P, Spector DL (2002) Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing. J Cell Biol 156:425–436 (10.1083/jcb.200107017) / J Cell Biol by P Sacco-Bubulya (2002)
  47. Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigo R (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 22:1616–1625 (10.1101/gr.134445.111) / Genome Res by H Tilgner (2012)
  48. Hepperger C, Mannes A, Merz J, Peters J, Dietzel S (2008) Three-dimensional positioning of genes in mouse cell nuclei. Chromosoma 117:535–551 (10.1007/s00412-008-0168-2) / Chromosoma by C Hepperger (2008)
  49. Murmann AE, Gao J, Encinosa M, Gautier M, Peter ME, Eils R, Lichter P, Rowley JD (2005) Local gene density predicts the spatial position of genetic loci in the interphase nucleus. Exp Cell Res 311:14–26 (10.1016/j.yexcr.2005.07.020) / Exp Cell Res by AE Murmann (2005)
  50. Küpper K, Kölbl A, Biener D et al (2007) Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116:285–306 (10.1007/s00412-007-0098-4) / Chromosoma by K Küpper (2007)
  51. Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12:439–445 (10.1016/S0960-9822(02)00695-4) / Curr Biol by JR Chubb (2002)
  52. Hakim O, Sung M-H, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL (2011) Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res 21:697–706 (10.1101/gr.111153.110) / Genome Res by O Hakim (2011)
  53. Lin S, Coutinho-Mansfield G, Wang D, Pandit S, Fu X-D (2008) The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol 15:819–826 (10.1038/nsmb.1461) / Nat Struct Mol Biol by S Lin (2008)
  54. Eskiw CH, Rapp A, Carter DRF, Cook PR (2008) RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci 121:1999–2007 (10.1242/jcs.027250) / J Cell Sci by CH Eskiw (2008)
  55. Eskiw CH, Fraser P (2011) Ultrastructural study of transcription factories in mouse erythroblasts. J Cell Sci 124:3676–3683 (10.1242/jcs.087981) / J Cell Sci by CH Eskiw (2011)
  56. Ghamari A, van de Corput MPC, Thongjuea S, van Cappellen WA, van Ijcken W, van Haren J, Soler E, Eick D, Lenhard B, Grosveld FG (2013) In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes Dev 27:767–777 (10.1101/gad.216200.113) / Genes Dev by A Ghamari (2013)
  57. Ferrai C, Xie SQ, Luraghi P, Munari D, Ramirez F, Branco MR, Pombo A, Crippa MP (2010) Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol 8:e1000270 (10.1371/journal.pbio.1000270) / PLoS Biol by C Ferrai (2010)
  58. Mitchell JA, Fraser P (2008) Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev 22:20–25 (10.1101/gad.454008) / Genes Dev by JA Mitchell (2008)
  59. Hakim O, Resch W, Yamane A et al (2012) DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 484:69–74 (10.1038/nature10909) / Nature by O Hakim (2012)
  60. Ploner C, Rainer J, Niederegger H, Eduardoff M, Villunger A, Geley S, Kofler R (2008) The BCL2 rheostat in glucocorticoid-induced apoptosis of acute lymphoblastic leukemia. Leukemia 22:370–377 (10.1038/sj.leu.2405039) / Leukemia by C Ploner (2008)
  61. Hepperger C, Otten S, von Hase J, Dietzel S (2007) Preservation of large-scale chromatin structure in FISH experiments. Chromosoma 116:117–133 (10.1007/s00412-006-0084-2) / Chromosoma by C Hepperger (2007)
  62. Solovei I, Cavallo A, Schermelleh L, Jaunin F, Scasselati C, Cmarko D, Cremer C, Fakan S, Cremer T (2002) Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). Exp Cell Res 276:10–23 (10.1006/excr.2002.5513) / Exp Cell Res by I Solovei (2002)
  63. Markaki Y, Smeets D, Fiedler S, Schmid VJ, Schermelleh L, Cremer T, Cremer M (2012) The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. BioEssays 34:412–426 (10.1002/bies.201100176) / BioEssays by Y Markaki (2012)
  64. Müller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, McNally JG (2004) Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol Cell Biol 24:9359–9370 (10.1128/MCB.24.21.9359-9370.2004) / Mol Cell Biol by WG Müller (2004)
  65. Telenius H, Pelmear AH, Tunnacliffe A, Carter NP, Behmel A, Ferguson-Smith MA, Nordenskjöld M, Pfragner R, Ponder BA (1992) Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosom Cancer 4:257–263 (10.1002/gcc.2870040311) / Genes Chromosom Cancer by H Telenius (1992)
  66. Solovei I, Walter J, Cremer M, Habermann F, Schermelleh L, Cremer T (2002) FISH, a practical approach. In: Beatty B, Mai S, Squire J (eds) Oxford University Press, pp 119–157
  67. Müller WG, Rieder D, Karpova TS, John S, Trajanoski Z, McNally JG (2007) Organization of chromatin and histone modifications at a transcription site. J Cell Biol 177:957–967 (10.1083/jcb.200703157) / J Cell Biol by WG Müller (2007)
  68. Bright Wilson EJR (1952) An introduction to scientific research. Dover Publications, Mineola, NY
  69. McManus KJ, Stephens DA, Adams NM, Islam SA, Freemont PS, Hendzel MJ (2006) The transcriptional regulator CBP has defined spatial associations within interphase nuclei. PLoS Comput Biol 2:e139 (10.1371/journal.pcbi.0020139) / PLoS Comput Biol by KJ McManus (2006)
Dates
Type When
Created 11 years, 11 months ago (Sept. 11, 2013, 9:14 a.m.)
Deposited 3 years, 5 months ago (March 5, 2022, 8:09 p.m.)
Indexed 1 year, 1 month ago (July 10, 2024, 3:09 a.m.)
Issued 11 years, 11 months ago (Sept. 12, 2013)
Published 11 years, 11 months ago (Sept. 12, 2013)
Published Online 11 years, 11 months ago (Sept. 12, 2013)
Published Print 11 years, 3 months ago (May 1, 2014)
Funders 0

None

@article{Rieder_2013, title={Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories}, volume={71}, ISSN={1420-9071}, url={http://dx.doi.org/10.1007/s00018-013-1465-3}, DOI={10.1007/s00018-013-1465-3}, number={9}, journal={Cellular and Molecular Life Sciences}, publisher={Springer Science and Business Media LLC}, author={Rieder, Dietmar and Ploner, Christian and Krogsdam, Anne M. and Stocker, Gernot and Fischer, Maria and Scheideler, Marcel and Dani, Christian and Amri, Ez-Zoubir and Müller, Waltraud G. and McNally, James G. and Trajanoski, Zlatko}, year={2013}, month=sep, pages={1741–1759} }