Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification

Abstract

Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). Here, we investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. We find that the ss locus is in a compact state in undifferentiated cells. An early enhancer drives ss transcription in all R7 precursors to open the ss locus. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives decompaction and then compaction represses transcription, controls stochastic cell fate specification.

Activating and repressing gene expression between chromosomes during stochastic fate specification

“…However, if transvection occurs late in development, we expected to observe no change in expression in precursor cells, but a change in the terminal % Ss ON R7s. We previously found that all precursors express ss in homozygous wildtype flies (Voortman, 2021).…”

“…To test the roles of the early and late enhancers in transvection, we tested alleles with deletions of the early enhancer (early enhD) or the late enhancer (late enhD) (Voortman, 2021). For these experiments, we used RNA fluorescent in situ hybridization (FISH) to assess changes in early ss expression in precursor cells in 3 rd instar larvae.…”

“…We predicted that, if transvection occurs early in precursor cells, we would see a change in the number of cells expressing ss RNA. Change in expression early is linked to a change in late Ss ON/OFF (Voortman, 2021). For example, a decrease in the number of precursor cells expressing ss will be reflected as a decrease in terminal Ss ON R7s.…”

“…Regulation of ss expression provides a unique opportunity to understand when and where transvection occurs during development. We found that expression of ss in a random subset of R7s is controlled by a dynamic interplay between transcription and chromatin earlier in development (Voortman, 2021). Photoreceptor specification occurs through a wave of differentiation during larval development (Ready et al, 1976;Tomlinson and Ready, 1987a;Wolff and Ready, 1991).…”

“…1G, 1H, "R7"). Ss ON R7s express ss and have open chromatin at the ss locus, whereas Ss OFF R7s repress ss and have compact chromatin (Voortman, 2021). The regulation of ss by two enhancers that function at distinct timepoints provides a model to elucidate the spatiotemporal roles of transvection.…”