Active and inactive genes localize preferentially in the periphery of chromosome territories.

Abstract

Abstract. The intranuclear position of a set of genes was analyzed with respect to the territories occupied by the whole chromosomes in which these genes are localized. Genes and their respective chromosome territories were simultaneously visualized in three-dimensionally preserved nuclei applying dual color fluorescence in situ hybridization. Three coding (DMD, MYH7, and HBB) and two noncoding sequences (D1Z2 and an anonymous sequence) were analyzed in four different cell types, including cells where DMD and MYH7 are actively transcribed. Spatial analysis by confocal laser scanning microscopy revealed that the genes are preferentially located in the periphery of chromosome territories. This positioning was independent from the activity of the genes. In contrast, the nonexpressed anonymous fragment was found randomly distributed or localized preferentially in the interior of the corresponding chromosome territory. Furthermore, the distribution of the analyzed genes within the territorial peripheries was found to be highly characteristic for each gene, and, again, independent from its expression. The impact of these findings with regard to the three-dimensional arrangement of the linear DNA string within chromosome territories, as well as with respect to a putative nuclear subcompartment confining gene expression, are discussed.'~EtPuIrTeE intensive efforts to decode the linear strucof complex genomes, up to the present day little is known about the three-dimensional genome organization within the cell nuclei of higher organisms. A territorial organization of interphase chromosomes has already been postulated by early cytologists such as Carl Rabl and Theodor Boveri (for review see Cremer, 1985), but this concept was mainly ignored in the 1960's and 70's (see e.g., Comings, 1980). The territorial organization was first shown indirectly by experiments, in which damaged regions of microirradiated cell nuclei, visualized in the subsequently prepared metaphase chromosomes, were found to be locally clustered (Zorn et al., 1979;Cremer et al., 1982). The chromosome territories were later visualized directly by means of in situ hybridization in interspecies somatic hybrid cells (Manuelidis, 1985;Schardin et al., 1985). Application of chromosome painting protocols subsequently proved that territorial organization of chromosomes occurs also in nonhybrid cells of mammalian (Cremer et al., 1988; Lichter et al., 1988a,b; Please address all correspondence to P. Lichter, Abteilung Organisation komplexer Genome, DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Pinkel et al., 1988) and plant (Schwarzacher et al., 1989;Leitch et al., 1990) origin. However, the spatial organization of the linear DNA molecule within a chromosome territory remains unclear. Based on the analysis of nuclear distances between DNA segments from the same chromosome, it has been suggested that the spatial position of chromatin segments within a chromosome territory follows a random distribution (van den Engh et al., 1992;Yokota et al., 1995;Sa...

The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

“…Although a body of evidence supports that genes are found on the border of chromosome territories (19,20,(49)(50)(51); specific genes have been shown to express from either inside, on the periphery or well outside of the territory (52)(53)(54). Other reports show that sequences (particularly large clusters of genes) move from a more internal to an external location upon transcriptional activation (53,(55)(56)(57).…”

“…The genes are found outside of the XIST RNA (yellow), which extends beyond the Barr body, the visible manifestation of the heterochromatin. 49,50,58,59) and splicing and transcription factors localize (22,49,51,60,61). The act of silencing and condensing the inner core of Xi may make the existing concentration of protein-coding genes in the peripheral region more pronounced and observable.…”

Form follows function: the genomic organization of cellular differentiation

“…1). Initial studies revealed that genes are preferentially positioned at territory surfaces, whereas intergenic DNA is found within the CT Kurz et al 1996). These observations led to the idea that an intervening compartment runs throughout the nucleus in the space between the discrete CTs, creating an interchromosome domain enriched for the nuclear bodies involved in transcription and splicing .…”

The Rb/chromatin connection and epigenetic control: opinion

“…In the interphase nucleus, individual chromosomes occupy speci®c spaces referred to as chromosome territories (Schardin et al, 1985). The active genes are preferentially localized either to the periphery of these chromosome territories or in the central nucleoplasm (Kurz et al, 1996;Wansink et al, 1996; for review see Lamond and Earnshaw, 1998). During interphase, there are two structural forms of chromatin: euchromatin, which is in a decondensed state and transcriptionally active, and heterochromatin (including centromeric and telomeric regions), which is condensed and generally transcriptionally inactive (reviewed in Gregory and Horz, 1998;Kadonaga, 1998;Wol e and Pruss, 1996).…”