Association of Transcriptionally Silent Genes with Ikaros Complexes at Centromeric Heterochromatin

Abstract

Ikaros proteins are required for normal T, B, and NK cell development and are postulated to activate lymphocyte-specific gene expression. Here we examined Ikaros distribution in the nucleus of B lymphocytes using confocal microscopy and a novel immunofluorescence in situ hybridization (immuno-FISH) approach. Unexpectedly, Ikaros localized to discrete heterochromatin-containing foci in interphase nuclei, which comprise clusters of centromeric DNA as defined by gamma-satellite sequences and the abundance of heterochromatin protein-1 (HP-1). Using locus-specific probes for CD2, CD4, CD8alpha, CD19, CD45, and lambda5 genes, we show that transcriptionally inactive but not transcriptionally active genes associate with Ikaros-heterochromatin foci. These findings support a model of organization of the nucleus in which repressed genes are selectively recruited into centromeric domains.

Nuclear repositioning marks the selective exclusion of lineage‐inappropriate transcription factor loci during T helper cell differentiation

“…In approximately one third of resting CD4 T cells isolated freshly ex vivo, the GATA-3 locus was associated with centromeric heterochromatin domains, as defined by a csatellite repeat probe (the major satellite repeat sequences that define centromeric heterochromatin in the mouse) [4]. Association of GATA-3 with centromeric heterochromatin was seen in a similar fraction of CD4 T cells activated in vitro for 3-4 days under nonpolarizing conditions (Fig.…”

“…The developmental history of cells is reflected in epigenetic modifications [1], such as DNA (CpG) methylation [2], the packaging of DNA in chromatin, post-translational modifications of chromatin proteins [3], and the spatial partitioning of gene loci into transcriptionally permissive and repressive domains within the nucleus [4][5][6].…”

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

“…In fact, the chromosomal DNA showing the highest GC level is endowed with the highest gene densities, early replication during the S phase of the cell cycle, and a more open chromatin structure, in contrast to the GC-poorest DNA that has the opposite features (Ferreira et al 1997;Sadoni et al 1999;Saccone et al, 2002;Tanabe et al 2002a;Boutanaev et al 2005;Foster and Bridger 2005;Petrova et al 2006). The compartmentalization of the cell nucleus is also associated with gene expression activity, with transcripts and splicing snRNPs preferentially located at the nuclear interior, whereas the nuclear periphery, largely occupied by heterochromatin, is generally transcriptionally inactive (Strouboulis and Wolffe 1996; Brown et al 1997;Andrulis et al 1998;Cockell and Gasser 1999;Lukasova et al 2002;Foster and Bridger 2005). A striking example, in this regard, concerns the inactive X chromosome in mammalian female cells, which is typically located towards the nuclear envelope forming the very compact structure of the Barr body, but with a large number of genes located away from the bulk of the chromosome territory (Clemson et al 2006).…”

Three-dimensional positioning of genes in mouse cell nuclei

“…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).…”