Single-cell c-myc gene expression in relationship to nuclear domains Eva Ba´rtova ´* , Andrea Harnicˇarova´, Jana Krejcˇı ´, Ludeˇk Strasˇa´k & Stanislav Kozubek Institute of Biophysics, Academy of Sciences of the Czech Republic, Kra´lovopolska´135, CZ-612 65, Brno, Czech Republic; Tel: +420-5-41517141; Fax: +420-5-41240498; E-mail: bartova@ibp.cz * Correspondence Received 12 October 2007. Received in revised form and accepted for publication by Herbert Macgregor 17 December 2007 Key words: c-myc gene, nuclear speckles, nucleolus, promyelocytic leukaemia body, transcription site 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 G 1 - 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 charac- terized 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 õ20% 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 õ60% 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 õ20% 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. Abbreviations c-myc T complex(es) involving c-myc transcripts DEPC diethyl pyrocarbonate DMs double minute chromosomes FISH fluorescence in situ hybridization HSA Homo sapiens autosome HSR homogeneously staining region IGCs interchromatin granule clusters PAC P1-derived artificial chromosome PML promyelocytic leukaemia RNAP II RNA polymerase II SDS sodium dodecyl sulfate Introduction Studies on the structural organization of the cell nucleus in relation to transcription and pre-mRNA processing are among the main focus of chromatin biology (Xing et al. 1995, Huang & Spector 1996, summarized by Belmont 2003, Shav-Tal et al. 2004, Bridger et al. 2005). Data on the relationship between the spatial organization of RNA synthesis, processing and transport provide valuable informa- tion on molecular mechanisms of RNA metabolism Chromosome Research (2008) 16:325Y343 # Springer 2007 DOI: 10.1007/s10577-007-1196-0