The three-dimensional architecture of Hox cluster silencing

Abstract

Spatial chromatin organization is emerging as an important mechanism to regulate the expression of genes. However, very little is known about genome architecture at high-resolution in vivo. Here, we mapped the three-dimensional organization of the human Hox clusters with chromosome conformation capture (3C) technology. We show that computational modeling of 3C data sets can identify candidate regulatory proteins of chromatin architecture and gene expression. Hox genes encode evolutionarily conserved master regulators of development which strict control has fascinated biologists for over 25 years. Proper transcriptional silencing is key to Hox function since premature expression can lead to developmental defects or human disease. We now show that the HoxA cluster is organized into multiple chromatin loops that are dependent on transcription activity. Long-range contacts were found in all four silent clusters but looping patterns were specific to each cluster. In contrast to the Drosophila homeotic bithorax complex (BX-C), we found that Polycomb proteins are only modestly required for human cluster looping and silencing. However, computational three-dimensional Hox cluster modeling identified the insulator-binding protein CTCF as a likely candidate mediating DNA loops in all clusters. Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation.

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

“…Th is contrasts with our results, which suggest that contact between promoters in the Irx clusters occurs in a similar manner in tissues independently of whether they express Irx genes, probably facilitating either their coactivation or their corepression. Moreover, our data show that the architecture of the two paralogous clusters is similar, whereas the architecture of the various human paralogous HOX clusters appears to be specifi c in each case 40 . Finally, it remains to be shown whether, as we show for the Irx clusters, the 3D architecture of orthologous Hox cluster is conserved.…”

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

“…Therefore, the coverage of specific parts of the cluster by polycomb complexes, depending on the proximal versus distal position of the cells (8,16) and observed in other functional contexts (30,37,38), does not seem to significantly influence its level of compaction. The distances apparently associated with these elongated forms correspond to previous distance predictions established by mathematical modeling (29).…”

The regulation of Hox gene expression during animal development

“…In particular, inactive and active areas of the Hox cluster segregate into separate domains. Inactive areas keep their mutual interactions but lose contact with active regions of the same cluster (Ferraiuolo et al, 2010;Noordermeer et al, 2011;Montavon et al, 2011). Interestingly, interactions were still observed throughout H3K4m3-rich active areas of the Hox clusters (Noordermeer et al, 2011;Montavon et al, 2011).…”

“…Analyses of the Hox clusters in undifferentiated human embryonal carcinoma and mouse ESCs using chromosome conformation capture approaches, revealed strong chromatin interactions spanning the whole cluster (Ferraiuolo et al, 2010;Noordermeer et al, 2011), indicating that inactive vertebrate Hox clusters might also be packed together within a specific nuclear compartment. A similar conclusion emerged from fluorescent in situ hybridisation (FISH) studies showing that 3Ј and 5Ј areas of the inactive Hoxb and Hoxd clusters localise together within their respective chromosomal territory (i.e.…”

“…Activation of Hox gene expression both in differentiating cells and in the developing tail and limb buds is associated with major structural changes in the Hox cluster chromatin (Chambeyron and Bickmore, 2004;Chambeyron et al, 2005;Eskeland et al, 2010;Ferraiuolo et al, 2010;Montavon et al, 2011;Morey et al, 2007;Noordermeer et al, 2011). In particular, inactive and active areas of the Hox cluster segregate into separate domains.…”