Transcription initiation drives dosage compensation establishment and maintenance in male Drosophila

Dosage compensation (DC) in Drosophila equalizes X chromosome-linked gene expression via the male-specific lethal complex, which acetylates histone 4 lysine-16 on the male X chromosome. How DC is established during early embryogenesis remains obscure, largely due to the difficulty of obtaining sufficient sex-specific material at early embryonic stages. Here, we developed a high-throughput embryo sorting strategy and combined newly synthesized RNA-sequencing and RNA polymerase II (Pol II) profiling to investigate the mechanisms underlying the onset of DC in vivo. We found that changes in transcription initiation occur before detectable differences in transcriptional pausing or elongation and represent the primary determinant of enhanced mRNA output during DC establishment. It had hitherto been unclear whether DC establishment and maintenance exerted similar or distinct effects on transcriptional kinetics. Extending genome-wide profiling to S2 cells, we uncovered Pol II initiation as a general principle underlying both inception and perpetuation of DC-driven transcriptional up-regulation.