Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases <i>DDX3X</i> and <i>DDX3Y</i>

The Y-linked gene <i>DDX3Y</i> and its X-linked homolog <i>DDX3X</i> survived the evolution of the human sex chromosomes from ordinary autosomes. <i>DDX3X</i> encodes a multifunctional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, <i>DDX3X</i> is extraordinarily dosage sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y Chromosomes increases, <i>DDX3X</i> transcript levels fall; conversely, when the number of X Chromosomes increases, <i>DDX3Y</i> transcript levels fall. In 46,XY cells, CRISPRi knockdown of either <i>DDX3X</i> or <i>DDX3Y</i> causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in <i>DDX3X</i> transcript levels. Thus, perturbation of either <i>DDX3X</i> or <i>DDX3Y</i> expression is buffered: by negative cross-regulation of <i>DDX3X</i> and <i>DDX3Y</i> in 46,XY cells and by negative auto-regulation of <i>DDX3X</i> in 46,XX cells. <i>DDX3X</i>-<i>DDX3Y</i> cross-regulation is mediated through mRNA destabilization-as shown by metabolic labeling of newly transcribed RNA-and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) <i>DDX3X</i> gene transmuted into auto- and cross-regulation of <i>DDX3X</i> and <i>DDX3Y</i> as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.