Atrx safeguards genome architecture and prevents ltr-driven gene activation

ATRX is a chromatin remodeler with diverse functions in histone H3.3 deposition, silencing of repetitive elements, and genome stability (Hoelper et al., 2017; Voon and Wong, 2016). ATRX regulates DNA methylation and binding of the architectural protein CTCF at imprinted genes (Gibbons et al., 2000; Kernohan et al., 2010), but whether it has a larger role in genome organization is unclear. Here, we use an ATRX knockout model to probe the effects of ATRX loss on genome-wide CTCF localization and 3D chromatin structure. We find that ATRX loss results in widespread changes in both CTCF and DNA methylation associated with dysregulation of H3.3 deposition and relocalization of the HIRA complex. Furthermore, we observe profound alterations to genome organization at every scale, from blurring of A/B compartments to restructuring of TADs and chromatin loops. While some of these changes are associated with CTCF dysregulation, others are linked to weakening of replication timing and derepression of long terminal repeat retrotransposons. Our findings establish ATRX as a regulator of genome organization in development and disease.