Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicasesDDX3XandDDX3Y

Abstract

AbstractThe Y-linked geneDDX3Yand its X-linked homologDDX3Xsurvived the evolution of the human sex chromosomes from ordinary autosomes.DDX3Xencodes a multi-functional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs,DDX3Xis extraordinarily dosage-sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y chromosomes increases,DDX3Xtranscript levels fall; conversely, when the number of X chromosomes increases,DDX3Ytranscript levels fall. In 46,XY cells, CRISPRi knockdown of eitherDDX3XorDDX3Ycauses transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase inDDX3Xtranscript levels. Thus, perturbation of eitherDDX3XorDDX3Yexpression is buffered – by negative cross-regulation ofDDX3XandDDX3Yin 46,XY cells, and by negative auto-regulation ofDDX3Xin 46,XX cells.DDX3X-DDX3Ycross-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)DDX3gene transmuted into auto- and cross-regulation ofDDX3XandDDX3Yas these sex-linked genes evolved from ordinary alleles of their autosomal precursor.