Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP

Abstract

Chromosomes and genes are nonrandomly arranged within the mammalian cell nucleus. However, the functional significance of nuclear positioning in gene expression is unclear. Here we directly probed the relationship between nuclear positioning and gene activity by comparing the location of the active and inactive copies of a monoallelically expressed gene in single cell nuclei. We demonstrate that the astrocyte-specific marker GFAP (glial fibrillary acidic protein) is monoallelically expressed in cortical astrocytes. Selection of the active allele occurs in a stochastic manner and is generally maintained through cell division. Taking advantage of the monoallelic expression of GFAP, we show that the functionally distinct alleles occupy differential radial positions within the cell nucleus and differentially associate with intranuclear compartments. In addition, coordinately regulated astrocyte-specific genes on distinct chromosomes spatially associate in their inactive state and dissociate upon activation. These results provide direct evidence for function-related differential positioning of individual gene alleles within the interphase nucleus.[Keywords: Monoallelic expression; spatial gene positioning; nuclear architecture; astrocyte] Supplemental material is available at http://www.genesdev.org.

The role of nuclear organization in cancer

“…There are numerous reports of active genes being preferentially located at the nuclear interior and inactive genes at the periphery [14][15][16]. These have led to the suggestion that the nuclear interior is generally permissive for transcription, while the nuclear periphery is transcriptionally repressive, possibly due to the presence of heterochromatin at the nuclear lamina.…”

Three-dimensional positioning of genes in mouse cell nuclei

“…They may involve differences between human and rodent nuclear organization. We next sought to analyze whether expressed gene loci colocalize with nuclear splicing factor speckles, as it was observed for several active genes (Nielsen et al 2002;Shopland et al 2003;Chuang et al 2006;Takizawa et al 2008). We codetected splicing speckles together with the oct3/4 gene locus in undifferentiated ES cells, in ES cells after 5 days of differentiation, and in terminally differentiated, postmitotic macrophages.…”

“…Studies investigating stably integrated transgenes in cultured hamster and mouse cells described cases where nuclear positioning was indeed expression dependent, with expressed loci more internal than inactive ones (Tumbar and Belmont 2001;Dietzel et al 2004;Chuang et al 2006). Nuclear positioning can be influenced by expression also for endogenous human or mouse gene loci, a fact maybe best illuminated by genes with monoallelic expression, where both genes show a different topology (Dietzel et al 1999;Takizawa et al 2008). Cases of gene repositioning upon transcriptional activation have been documented relative to their chromosome territory (Volpi et al 2000;Williams et al 2002;Chambeyron and Bickmore 2004), relative to centromeric heterochromatin (Brown et al 1997), for movement away from peripheral heterochromatin (Kosak et al 2002;Zink et al 2004;Ragoczy et al 2006;Williams et al 2006) and for other movements towards more central areas (Takizawa et al 2008).…”

“…Nuclear positioning can be influenced by expression also for endogenous human or mouse gene loci, a fact maybe best illuminated by genes with monoallelic expression, where both genes show a different topology (Dietzel et al 1999;Takizawa et al 2008). Cases of gene repositioning upon transcriptional activation have been documented relative to their chromosome territory (Volpi et al 2000;Williams et al 2002;Chambeyron and Bickmore 2004), relative to centromeric heterochromatin (Brown et al 1997), for movement away from peripheral heterochromatin (Kosak et al 2002;Zink et al 2004;Ragoczy et al 2006;Williams et al 2006) and for other movements towards more central areas (Takizawa et al 2008). However, expression has also been reported for genes at the nuclear periphery (Nielsen et al 2002;Ragoczy et al 2006) and a study using a transgene tethered to the nuclear lamina could show that this transgene maintains transcriptional activity (Kumaran and Spector 2008).…”

Characterization and dynamics of pericentromere-associated domains in mice

“…inactive (Brown et al 2001;Hewitt et al 2004;Takizawa et al 2008;Jost et al 2011). Moreover, some genes have been shown to be transcribed even when associated with chromocenters (Lundgren et al 2000;Sabbattini et al 2001), and several genes that are embedded in heterochromatin appear to rely on a heterochromatic environment for expression in Drosophila (Wakimoto and Hearn 1990;Lu et al 2000).…”