SETDB1 compacts the inactive X chromosome in part through silencing an enhancer in the IL1RAPL1 gene

The product of dosage compensation in human females is the compacted inactive X chromosome (Xi). Here we show that loss of SET domain bifurcated 1 (SETDB1) results in decompaction of the Xi territory coupled with reactivation on the Xi of a powerful enhancer within the 1.4 Mb interleukin-1 receptor accessory protein like 1 (IL1RAPL1) gene at Xp21.2. The enhancer is centrally located in a 0.5 Mb region corresponding to the 3’ third of the IL1RAPL1 locus that transitions from a heterochromatic territory to a euchromatic configuration on the Xi in the absence of SETDB1. This same region showing chromatin instability is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Immediately adjacent to the enhancer is an ERVL-MaLR element that drives bi-directional transcription of novel long sense and antisense transcripts. Deletion of the enhancer from the Xa (but not Xi), resulted in detection of bi-directional expression from the Xi coupled with decompaction of the chromosome territory, supporting a critical role for SETDB1 in maintaining this interval in a silent state to facilitate Xi compaction. Examination of three different histone modifications in parental and knock out cells, as well as rRNA-depleted total-RNA-Seq in the parental cells and two independent knock-out clones.