elegans embryos [ 59••]. An RNAi screen identified PTC124 mouse 29 factors that, when knocked-down, led to activation of a peripheral repressed reporter array. Interestingly, only 2 of these factors resulted in additional movement of the array into the nucleoplasm, demonstrating that movement is not required for gene activation. Conversely, movement of a reporter gene under an inactive promoter from the periphery was not accompanied by transcriptional activation [ 59••]. Therefore, while there is a correlation between gene expression levels and nuclear periphery positioning, the two processes are not necessarily dependent on each other. Additional characterization of the factors that are required

for gene positioning relative to the nuclear periphery and other nuclear structures represents an interesting area for future research. When

considering gene positioning, selleck kinase inhibitor either relative to topological associated domains, chromatin territories, or a nuclear structure such as the lamina, an important consideration is whether changes in gene position occur before or following changes in gene expression (Figure 2). For example, the HOX gene cluster in mammals change during differentiation from a single domain marked by H3K27me3 to a bimodal domain in which the active Hox genes occupy a separate region rich in H3K4me3 distinct from the inactive regions [60••]. However, it is unknown whether the structural changes that accompany gene activation are necessary for transcription to occur, or whether they are a secondary event stabilizing the gene expression program in the cells. The two alleles of the imprinted Kcnq1 locus have recently been shown to associate in early embryogenesis at sites of high RNA polymerase II occupancy [ 61]. This suggests a role for gene transcription

in mediating the pairing, however cause and effect again remain unknown. Similarly, the long noncoding RNAs TUG1 and MALAT1/NEAT2 have been implicated in the relocation of growth control genes between Polycomb bodies and interchromatin granule clusters [ 62]. Long range Urease chromosomal interactions between the ifrrγ cytokine gene and its receptor genes ifrrγR1 and ifrrγR2 are also associated with gene expression [ 63]. This interaction persists following inhibition of transcription with the RNA polymerase II inhibitor α-amanitin, implying that gene transcription is not required to maintain the intergenic interactions. However, it remains to be determined whether transcription is required for their establishment. Along these lines, chromatin looping may directly affect transcription, rather than being the result of transcriptional co-regulation. This was shown by zinc-finger mediated tethering of the GATA1 associated protein Ldb1, or merely its self-association domain, to the β-globin promoter in erythroid cells [ 64••].