Atrx promotes heterochromatin formation at retrotransposons

More than 50% of mammalian genomes consist of retrotransposon sequences. Silencing of retrotransposons by heterochromatin is essential to ensure genomic stability and transcriptional integrity. Here, we identified a short sequence element in intracisternal A particle (IAP) retrotransposons that is sufficient to trigger heterochromatin formation. We used this sequence in a genome-wide shRNA screen and identified the chromatin remodeler Atrx as a novel regulator of IAP silencing. Atrx binds to IAP elements and is necessary for efficient heterochromatin formation. In addition, Atrx facilitates a robust and largely inaccessible heterochromatin structure as Atrx knockout cells display increased chromatin accessibility at retrotransposons and non-repetitive heterochromatic loci. In summary, we demonstrate a direct role of Atrx in the establishment and robust maintenance of heterochromatin. Synopsis Atrx contributes to retrotransposon silencing in ES cells by promoting inaccessible heterochromatin formation. The data also suggest that retrotransposon silencing requires the histone chaperone Daxx but is independent of histone H3.3. We identify a small heterochromatin initiation site in IAP-Ez retrotransposons. Atrx assists in Setdb1-/Trim28-dependent heterochromatin establishment and maintenance. A locus-specific chromatin accessibility assay reveals that Atrx-deficient heterochromatin is more accessible and vulnerable to challenges. Atrx contributes to retrotransposon silencing in ES cells by promoting inaccessible heterochromatin formation. The data also suggest that retrotransposon silencing requires the histone chaperone Daxx but is independent of histone H3.3.