Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally-deposited pioneer factor called CLAMP (Chromatin linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development.
Sequencing data have been deposited in GEO under accession codes #GSE220455 and #GSE220439All data generated or analyzed during this study are included in the manuscript and supporting file; Source Data files have been provided for Figures 2-figure Supplement 3, Figure 5, and Figure 6Source data used to generate all the figures, graphs, and Venn diagrams are provided in Supplementary Data Tables S1-S7
Effect of loss of transcription factor CLAMP on sex-specific splicing in Drosophila third instar larvae (L3) stageNCBI Gene Expression Omnibus, GSE220455.
Identifying splicing targets of CLAMP by mRNA-sequencingNCBI Gene Expression Omnibus, GSE220439.
Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMPNCBI Gene Expression Omnibus, GSE102922.
Targeting of the dosage-compensated male X-chromosome during early Drosophila developmentNCBI Gene Expression Omnibus, GSE133637.
- Mukulika Ray
- Erica Larschan
- Ashley Mae Conard
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Luisa Cochella, Johns Hopkins University, United States
© 2023, Ray et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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