Two distinct waves of transcriptome and translatome changes drive germline stem cell differentiation

The tight control of fate transitions during stem cell differentiation is essential for proper
tissue development and maintenance. However, identifying how the multilayered regulation
of gene expression programmes orchestrates stem cell differentiation in vivo remains
elusive, because of the challenges in studying sparsely distributed adult stem cells in a
systematic manner. Here, we synchronised Drosophila female germline stem cell (GSC)
differentiation in vivo to perform in-depth transcriptome and translatome analyses at high
developmental resolution. This characterisation revealed widespread and dynamic changes
in mRNA level, promoter usage, exon inclusion, and translation efficiency. Transient
expression of the master regulator, Bam, drives a first wave of expression changes, primarily
modifying the cell cycle programme. Surprisingly, as Bam levels recede, differentiating cells
return to a remarkably stem cell-like transcription and translation programme, with a few
crucial changes feeding into a second phase driving terminal differentiation to form the
oocyte. Altogether, these findings reveal that rather than a unidirectional accumulation of
changes, the in vivo differentiation programme relies on distinctly regulated and
developmentally sequential waves.