bioRxiv preprint doi: https://doi.org/10.1101/2020.09.11.292573; this version posted September 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Differentiation Hsing-Chun Chen1, Yi-Ru Li1, Hsiao Wen Lai1, Hsiao Han Huang1, Sebastian D. Fugmann1,2,4, Shu Yuan Yang1,2,3* 1Department and 2Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan 3Departmen of Gynecology and 4Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan *To whom correspondence should be directed:
[email protected] Abstract Germ cells in D. melanogaster are specified maternally shortly after fertilization and are transcriptionally quiescent until their zygotic genome is activated to sustain further development. To understand the molecular basis of this process, we analyzed the progressing transcriptomes of early male and female germ cells at the single-cell level between germline specification and coalescence with somatic gonadal cells. Our data comprehensively covered zygotic activation in the germline genome, and analyses on genes that exhibit germline-restricted expression revealed that polymerase pausing and differential RNA stability are important mechanisms that establish gene expression differences between the germline and soma. In addition, we observed an immediate bifurcation between the male and female germ cells as zygotic transcription begins. The main difference between the two sexes is an elevation in X chromosome expression in females relative to males signifying incomplete dosage compensation with a few select genes exhibiting even higher expression increases.