Distinct nuclear arrangement of active and inactive c-myc genes in control and differentiated colon carcinoma cells

The role of nuclear organization in cancer

“…A similar inversion of chromosomes 18 and 19 has been found in about onethird of papillary thyroid carcinoma cells but not in normal thyroid cells [26]. Furthermore, while activated oncogenes are found in some cancers to be preferentially located in the nuclear interior when compared to control cells [27][28][29], others appear at the nuclear periphery [30]. In an extensive study of a cultured model of breast cancer, genes were identified which become repositioned during early tumourigenesis.…”

Epigenome and chromatin structure in human embryonic stem cells undergoing differentiation

“…Peripheral repositioning of centromeres is the most common structural change associated with differentiation in human and mouse cell types (Chaly and Munro, 1996;Bá rtová et al, 2001;Harničarová et al, 2006). Wiblin et al (2005) reported that the proportion of centromeres located close to the nuclear periphery in hESCs is smaller than that in highly differentiated B-cells.…”

“…The slides were then washed for 15 min in PBS, and preparations were incubated with one of the following antibodies: anti-H3K4me2 (#07-030, Upstate), anti-H3K4me3 (#ab8580-2b, Abcam), anti-H3K9me1 (#ab9045-25, Abcam), anti-H3K9me2 (#07-212, Upstate), anti-H3K9me3 (#07-442, Upstate), anti-H3K9Ac (#06-942, Upstate), anti-H3K27me2 (#07-322, Upstate), anti-H3K27me3 (#07-449, Upstate), anti-H3K79me1 (#ab2886-25, Abcam), and mouse monoclonal anti-CENP-A (#ab13939, Abcam). Nucleoli were detected using mouse monoclonal antibody to fibrillarin (#ab12367, Abcam) and RNA polymerase II (RNAP II) -pos-itive regions were recognized with the aid of mouse monoclonal antibody against phosporylated form of RNAP II (#ab24759, Abcam; Harničarová et al, 2006). After an overnight incubation of preparations with primary antibody at 4°C, appropriate secondary antibody was applied.…”

“…Probes (Poseidon FISH DNA probes) for centromere 15 (KBI-20015), centromere 17 (KBI-20017), and centromeres 1/5/19 (KBI-20026) were obtained from Kreatech Diagnostics (Amsterdam, the Netherlands). The cells used in these experiments were fixed in 4% formaldehyde in PBS for 10 min, and the three-dimensional FISH technique was performed as described elsewhere (Harničarová et al, 2006). MEFs and hESCs were distinguished by using the counterstain, TO-PRO (R)-3 iodide (0.04 g/ml, Molecular Probes), which labeled whole interphase nuclei and centromeric heterochromatin arranged into chromocenters (Alcobia et al, 2003) in MEFs.…”

Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes

“…Examples include global effects like chromosome territories (Foster and Bridger 2005;Cremer et al 2006) and transcription factories (Faro-Trindade and Cook 2006), and specific effects such as telomeres and centromeres at the yeast nuclear periphery (Heun et al 2001a;Hediger et al 2002), the large ribosomal DNA repeats at the nucleoli of all organisms (Shaw et al 1995), and the 5S rDNA at or near the nucleoli of many organisms . Multiple genes alter their position when transcriptionally activated (Buchenau et al 1997;Brown et al 1999;Volpi et al 2000;Kosak et al 2002;Casolari et al 2004Casolari et al , 2005Harnicarova et al 2006), and some genes are brought together with linearly distant enhancer elements (Liu and Garrard 2005;Spilianakis et al 2005;Liu and Francke 2006;Su et al 2006). In some cases, genes that are coregulated but not linearly connected are brought together in three dimensions, including ␤-globin genes that are found clustered when active (Brown et al 2006), and the nucleolar clustering of most of the 274 tRNA genes in Saccharomyces cerevisiae, which are transcribed by RNA polymerase III (pol III) (Thompson et al 2003;L.…”