Sex-specific transcriptome dynamics of Anopheles gambiae during embryonic development [Ag55 ChIP-Seq]
Malaria-transmitting mosquitoes are extremely sexually dimorphic in their anatomy and behaviour. Sex-specific gene expression in Anopheles gambiae is well-studied in adult stages, but its onset during embryogenesis, apart from sex-determination factors like Yob, remains largely unknown. Here, we report a comprehensive single-embryo transcriptome atlas of A. gambiae males and females to understand the earliest stages of establishing the sex-specific expression networks. Our dataset reveals embryonic RNA isoform diversity including a global shift towards distal alternative polyadenylation (APA) events sites during the maternal-to-zygotic genome transition. Sex-biased gene expression and alternative splicing are limited during embryogenesis, with most sex-specific patterns emerging post-embryonically. X chromosome dosage compensation is established shortly after zygotic genome activation concomitant with direct binding of the master regulator protein SOA to X-linked promoters. In contrast to DC regulators in Drosophila and mammals, we find rather weak evidence in Anopheles for early binding sites or distance-dependent patterns. Instead, both compensation and binding tend to occur locally and uniformly across genes and developmental stages. The most highly expressed genes tend to show the strongest SOA binding. We propose that the Anopheles dosage compensation system represents an extreme case of a gene-by-gene regulatory mechanism that operates at the chromosome-wide level. Overall design: ChIP-Seq samples are analyzed with two biological replicates per group. Input controls were used as negative controls for unspecific background signal.