RT Journal Article SR Electronic T1 Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome JF bioRxiv FD Cold Spring Harbor Laboratory SP 165340 DO 10.1101/165340 A1 G. Bonora A1 X. Deng A1 H. Fang A1 V. Ramani A1 R. Qiu A1 J. Berletch A1 G. N. Filippova A1 Z. Duan A1 J. Shendure A1 W.S. Noble A1 C.M. Disteche YR 2017 UL http://biorxiv.org/content/early/2017/07/19/165340.abstract AB The mammalian inactive X chromosome (Xi) condenses into a bipartite structure with two superdomains of frequent long-range contacts separated by a boundary or hinge region. Using in situ DNase Hi-C in mouse cells with deletions or inversions within the hinge we show that the conserved repeat locus Dxz4 alone is sufficient to maintain the bipartite structure and that Dxz4 orientation controls the distribution of long-range contacts on the Xi. Frequent long-range contacts between Dxz4 and the telomeric superdomain are either lost after its deletion or shifted to the centromeric superdomain after its inversion. This massive reversal in contact distribution is consistent with the reversal of CTCF motif orientation at Dxz4. De-condensation of the Xi after Dxz4 deletion is associated with partial restoration of TADs normally attenuated on the Xi, and with an increase in chromatin accessibility and CTCF binding, but few changes in gene expression, in accordance with multiple epigenetic mechanisms ensuring X silencing. We propose that Dxz4 represents a structural platform for frequent long-range contacts with multiple loci in a direction dictated by the orientation of a bank of CTCF motifs at Dxz4, which may work as a ratchet to form the distinctive bipartite structure of the condensed Xi.