Abstract
Nuclear locations of the c-myc gene and its transcripts (c-myc T) have been investigated in relation to nuclear domains involved in RNA synthesis and processing. Transcription of the c-myc gene appears to be linked to the late G1- and preferentially to S-phases of the cell cycle. The c-myc gene and its transcripts were positioned non-randomly within the interphase nucleus; additionally, c-myc RNA signals accumulated at nucleoli. Using oligo-probes, designed to exon II and exon III of the c-myc gene, single c-myc T was preferentially observed in human carcinoma HT29 and A549 cells. Conversely, human embryonal teratocarcinoma NTERA cells were characterized by the presence of multiple c-myc RNA signals located in both the nucleoli and nucleoplasm. When accumulated at nucleoli, c-myc T occupied the periphery of this organelle, though not those associated with the cultivation surface. In HT29 cells, approximately 80% of c-myc T co-localized with the RNAP II positive regions, so-called transcription factories. However, in ∼20% of the cells with c-myc transcripts, the c-myc T was released from the site of synthesis, and was not associated with either transcription factories or SC35 domains. In ∼60% of nuclei with c-myc T, these signals were located in close proximity to the SC35 regions, but promyelocytic leukaemia bodies were associated with c-myc T only in ∼20% of the nuclei. Taken together, c-myc RNA signals were positioned in the most internal parts of the cell nuclei preferentially associated with the nucleoli. Specific nuclear and nucleolar positioning probably reflects the kinetics of c-myc RNA metabolism.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Andersen JS, Lam YW, Leung AK et al. (2005) Nucleolar proteome dynamics. Nature 433: 77–83.
Bártová E, Kozubek S, Jirsová P et al. (2002) Nuclear structure and gene activity in human differentiated cells. J Struct Biol 139: 76–89.
Bártová E, Pacherník J, Harničarová A et al. (2005) Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases. J Cell Sci 118: 5035–5046.
Bártová E, Pacherník J, Kozubík A, Kozubek S (2007a) Differentiation-specific association of HP1alpha and HP1beta with chromocentres is correlated with clustering of TIF1beta at these sites. Histochem Cell Biol 127: 375–388.
Bártová E, Krejčí J, Harničarová A, Kozubek S (2007b) Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation 127: 375–388.
Belmont A (2003) Dynamics of chromatin, proteins, and bodies within the cell nucleus. Curr Opin Cell Biol 15: 304–310.
Bond VC, Wold B (1993) Nucleolar localization of myc transcripts. Mol Cell Biol 13: 3221–3230.
Brelvi ZS, Studzinski GP (1986) Coordinate expression of c-myc, c-myb, and histone H4 genes in reversibly differentiating HL 60 cells. J Cell Physiol 131: 43–49.
Bridger JM, Kalla C, Wodrich H et al. (2005) Nuclear RNAs confined to a reticular compartment between chromosome territories. Exp Cell Res 302: 180–193.
Brown JM, Leach J, Reittie JE et al. (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172: 177–187.
Chakalova L, Debrand E, Mitchell JA et al. (2005) Replication and transcription: shaping the landscape of the genome. Nat Rev Genet 6: 669–677.
Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18: 1119–1130.
Clemson CM, Lawrence JB (1996) Multifunctional compartments in the nucleus: insights from DNA and RNA localization. J Cell Biochem 62: 181–190.
Denis MM, Tolley ND, Bunting M et al. (2005) Escaping the nuclear confines: signal-dependent pre-mRNA splicing in anucleate platelets. Cell 122: 379–391.
Dietzel S, Schiebel K, Little G et al. (1999) The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity. Exp Cell Res 252: 363–375.
Dirks RW, de Pauw ES, Raap AK (1997) Splicing factors associate with nuclear HCMV-IE transcripts after transcriptional activation of the gene, but dissociate upon transcription inhibition: evidence for a dynamic organization of splicing factors. J Cell Sci 110: 515–522.
Fakan S (2004) The functional architecture of the nucleus as analysed by ultrastructural cytochemistry. Histochem Cell Biol 122: 83–93.
Galiová G, Bártová E, Kozubek S (2004) Nuclear topography of beta-like globin gene cluster in IL-3-stimulated human leukemic K-562 cells. Blood Cells Mol Dis 33: 4–14.
Gilbert N, Boyle S, Fiegler H et al. (2004) Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118: 555–566.
Guillot PV, Xie SQ, Hollinshead M, Pombo A (2004) Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells. Exp Cell Res 295: 460–468.
Harničarová A, Kozubek S, Pacherník J et al. (2006) Distinct nuclear arrangement of active and inactive c-myc genes in control and differentiated colon carcinoma cells. Exp Cell Res 312: 4019–4035.
He TC, Sparks AB, Rago C et al. (1998) Identification of c-MYC as a target of the APC pathway. Science 281: 1509–1512.
Hirose Y, Tacke R, Manley JL (1999) Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev 13: 1234–1239.
Huang S, Spector DL (1991) Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev 5: 2288–2302.
Huang S, Spector DL (1996) Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J Cell Biol 133: 719–732.
Kawai K, Viars C, Arden K et al. (2002) Comprehensive karyotyping of the HT-29 colon adenocarcinoma cell line. Genes Chromosomes Cancer 4: 1–8.
Kiesslich A, von Mikecz A, Hemmerich P (2002) Cell cycle-dependent association of PML bodies with sites of active transcription in nuclei of mammalian cells. J Struct Biol 140: 167–179.
Kozubek M, Kozubek S, Lukášová E et al. (1999) High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry 36: 279–293.
Kurz A, Lampel S, Nickolenko JE et al. (1996) Active and inactive genes localize preferentially in the periphery of chromosome territories. J Cell Biol 135: 1195–1205.
Lamond AI, Spector DL (2003) Nuclear speckles: a model for nuclear organelles. Nat Rev Mol Cell Biol 4: 605–612.
Lawrence JB, Singer RH, Marselle LM (1989) Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization. Cell 57: 493–502.
Levsky JM, Shenoy SM, Pezo RC, Singer RH (2002) Single-cell gene expression profiling. Science 297: 836–840.
Mahy NL, Perry PE, Bickmore WA (2002) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159: 753–763.
McCracken S, Fong N, Yankulov K et al. (1997) The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385: 357–361.
Neugebauer KM, Roth MB (1997) Transcription units as RNA processing units. Genes Dev 11: 3279–3285.
Osborne CS, Chakalova L, Brown KE et al. (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065–1071.
Pagano A, Castelnuovo M, Tortelli F et al. (2007) New small nuclear RNA gene-like transcriptional units as sources of regulatory transcripts. PLoS Genet 3,e1: 0174–0184.
Politz JC, Tuft RA, Pederson T, Singer RH (1999) Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol 9: 285–291.
Scheuermann MO, Tajbakhsh J, Kurz A et al. (2004) Topology of genes and nontranscribed sequences in human interphase nuclei. Exp Cell Res 301: 266–279.
Shav-Tal Y, Singer RH (2005) RNA localization. J Cell Sci 118: 4077–4081.
Shav-Tal Y, Singer RH, Darzacq X (2004) Imaging gene expression in single living cells. Nat Rev Mol Cell Biol 5: 855–861.
Shimizu N, Kawamoto JK, Utani K (2007) Regulation of c-myc through intranuclear localization of its RNA subspecies. Biochem Biophys Res Commun 359: 806–810.
Smith KP, Moen PT, Wydner KL et al. (1999) Processing of endogenous pre-mRNAs in association with SC35 domains is gene specific. J Cell Biol 144: 617–629.
Steinmetz EJ (1997) Pre-mRNA processing and the CTD of RNA polymerase II: the tail that wags the dog? Cell 89: 491–494.
Volpi EV, Chevret E, Jones T et al. (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.
Wang J, Shiels C, Sasieni P et al. (2004) Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions. J Cell Biol 164: 515–526.
Wiblin AE, Cui W, Clark AJ, Bickmore WA (2005) Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells. J Cell Sci 118: 3861–3868.
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.
Williams RR, Azuara V, Perry P et al. (2006) Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci 119: 132–140.
Wilson AJ, Velcich A, Arango D et al. (2002) Novel detection and differential utilization of a c-myc transcriptional block in colon cancer chemoprevention. Cancer Res 62: 6006–6010.
Xing Y, Johnson CV, Dobner PR, Lawrence JB (1993) Higher level organization of individual gene transcription and RNA splicing. Science 259: 1326–1330.
Xing Y, Johnson CV, Moen PT Jr et al. (1995) Nonrandom gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC35 domains. J Cell Biol 131: 1635–1647.
Zeng C, Kim E, Warren SL, Berget SM (1997) Dynamic relocation of transcription and splicing factors dependent upon transcriptional activity. EMBO J 16: 1401–1412.
Zhang G, Taneja KL, Singer RH, Green MR (1994) Localization of pre-mRNA splicing in mammalian nuclei. Nature 372: 809–812.
Zink D, Amaral MD, Englmann A et al. (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166: 815–825.
Zirbel RM, Mathieu UR, Kurz A et al. (1993) Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res 1: 93–106.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bártová, E., Harničarová, A., Krejčí, J. et al. Single-cell c-myc gene expression in relationship to nuclear domains. Chromosome Res 16, 325–343 (2008). https://doi.org/10.1007/s10577-007-1196-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10577-007-1196-0