Disruption of a boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation, whereas topological domains are largely unaffected
in absence of H3K27me3 [30••]. Moreover, another study showed that the 3D conformation of the X chromosome controls the initial transfer of the Xist RNA to distal X chromosome regions, which are not defined by specific DNA sequences [39]. On the other hand, chromosomal regions escaping X inactivation do not always localize outside the territory covered Vorinostat in vivo by Xist and, conversely, silencing can be maintained outside the Xist domain for a subset of the genes on the inactive X [40]. All these data suggest that sequence and gene specific cues cooperate with
3D chromatin organization in order to orchestrate the process of X inactivation. Dynamic topological domains are also involved in the regulation of Hox gene expression, which controls the patterning of the vertebrate antero-posterior body axis. By probing loops established between the IDH cancer active part of the Hoxd cluster with elements dispersed throughout the nearby gene desert, it was possible to identify novel Hoxd enhancers, which disperse in the gene desert to form a regulatory archipelago that coordinately regulates Hoxd gene expression in digits [41]. The internal
structure of Hox gene clusters was further investigated by a high resolution 4C approach. Inactive Sorafenib Hox genes associate into a single topological domain delimited from flanking regions. During activation, Hox genes progressively cluster into another compartment. This structural switch matches the transition in chromatin marks, with the H3K27me3 repressive mark initially covering repressed Hox genes, whereas their transcriptional activation associates with H3K4me3 deposition [29•]. Further analysis of the HoxD cluster architecture reveals a functional switch between topological domains. During mouse limb development, a first wave of HoxD transcription specifies arm and forearm patterning and a late wave of transcription occurs when digits form. A subset of HoxD genes in the middle of the cluster initially interacts with the telomeric domain and later establishes new contacts with the centromeric domains [31••]. Another work studying a long intergenic noncoding RNA HOTTIP transcribed from the 5′ tip of the HoxA locus also highlights the importance of 3D architecture of Hox gene clusters. Chromosomal looping brings the noncoding RNA HOTTIP into close proximity to its target genes and this chromatin proximity is necessary and sufficient for HOTTIP-mediated transcriptional activation [42].
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