Chromosome-specific adaptations of RNA stability and the roles of the roX RNAs in dosage compensation

Sex chromosomes evolved from an ancient pair of autosomes and the Y chromosome lost most of its genetic information in the process. This created two kinds of genomic imbalances: the first one between males (XY) and females (XX) and the second one between the sex chromosomes and the autosomes (X:AA). In mammals, the male:female dosage compensation is achieved through the random inactivation of one of the two female X chromosomes. Through genome-wide studies of RNA stability, we show that one of the strategies used for the X:AA dosage compensation is to specifically increase the RNA stability of its X chromosome transcripts in both sexes. We also observe an increase in ribosome density on the X chromosome´s transcripts and propose that a large part of dosage compensation in mammals happens at the translational level. In D. melanogaster (fruit flies), dosage compensation is achieved through a two-fold upregulation of transcription from the male X chromosome. This solves the male:female and the X:AA imbalance at once. We did not find any evidence for RNA stability having a role in fly dosage compensation. However, our data allowed us to propose two new RNA stability mediated mechanisms for the general regulation of gene expression. The first one is a buffering mechanism that responds to detrimental changes in transcription by increasing RNA stability upon decrease in transcription and vice versa. The second mechanism enhances the adapted differential transcription between the sexes by shifting RNA stability accordingly. The MSL complex is a nucleoprotein complex composed of at least 5 proteins and two non-coding RNAs (roX1 and roX2). It is only assembled in males and specifically targets their X chromosome, promoting upregulation of transcription. Each and every protein is essential for male viability, but each roX RNA can be deleted without exhibiting any phenotype. However, the deletion of both also kills males specifically. Despite this redundancy, the roX RNAs have been shown to be expressed at different times during development and they differ in size and sequence. We analyzed the differential expression in roX1, roX2 and roX1 roX2 double mutants in regard to distance to high affinity binding sites of the MSL complex, MSL binding strength and replication timing and showed that the roX RNAs fulfill separate functions in dosage compensation. We also discovered and characterized two ectopic female specific high affinity binding sites for the protein POF (painting of fourth) which specifically targets and upregulates the transcription from the fourth chromosome of D. melanogaster. We named these sites PoX1 and PoX2 because they are situated in the vicinity of roX1 and roX2 loci and we postulate that they constitute molecular evolutionary links between dosage compensation and the autosome specific gene regulation of the fourth chromosome