The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes

Abstract

The gene products that drive early development are critical for setting up developmental trajectories in all animals. The earliest stages of development are fueled by maternally provided mRNAs until the zygote can take over transcription of its own genome. In early development, both maternally deposited and zygotically transcribed gene products have been well characterized in model systems. Previously, we demonstrated that across the genus Drosophila, maternal and zygotic mRNAs are largely conserved but also showed a surprising amount of change across species, with more differences evolving at the zygotic stage than the maternal stage. In this study, we use comparative methods to elucidate the regulatory mechanisms underlying maternal deposition and zygotic transcription across species. Through motif analysis, we discovered considerable conservation of regulatory mechanisms associated with maternal transcription, as compared to zygotic transcription. We also found that the regulatory mechanisms active in the maternal and zygotic genomes are quite different. For maternally deposited genes, we uncovered many signals that are consistent with transcriptional regulation at the level of chromatin state through factors enriched in the ovary, rather than precisely controlled gene-specific factors. For genes expressed only by the zygotic genome, we found evidence for previously identified regulators such as Zelda and GAGA-factor, with multiple analyses pointing toward gene-specific regulation. The observed mechanisms of regulation are consistent with what is known about regulation in these two genomes: during oogenesis, the maternal genome is optimized to quickly produce a large volume of transcripts to provide to the oocyte; after zygotic genome activation, mechanisms are employed to activate transcription of specific genes in a spatiotemporally precise manner. Thus the genetic architecture of the maternal and zygotic genomes, and the specific requirements for the transcripts present at each stage of embryogenesis, determine the regulatory mechanisms responsible for transcripts present at these stages.

Evolved Differences in cis and trans Regulation Between the Maternal and Zygotic mRNA Complements in the Drosophila Embryo

“…M1BP is involved in transcriptional regulation and RNA polymerase II pausing at the promoter of genes ( Li and Gilmour 2013 ), which may also be associated with regulating chromatin state ( Ramírez et al 2018 ). Our findings are consistent with previous studies that identified the enrichment of binding sites for M1BP, BEAF-32, and Dref in the promoter regions of genes that are maternally deposited ( Chen et al 2013 ; Omura and Lott 2020 ). These binding sites have also been associated with housekeeping genes ( Zabidi et al 2015 ), and the pool of maternal transcripts is enriched with housekeeping genes ( Liu et al 2014 ).…”

“…The oocyte itself is thought to be largely transcriptionally silent ( Navarro-Costa et al 2016 ). What we found here, and what was also found in another study investigating binding motifs in maternal factors across the Drosophila genus using computational methods ( Omura and Lott 2020 ), is that maternal transcription is associated with trans factors annotated to be insulators and that interact with TADs. This provides evidence that maternal transcription may be controlled broadly at the level of chromatin state.…”

“…Transcriptional regulation at the maternal stage may be broadly determined by regulation at the level of chromatin, as evidenced in this work and by another study ( Omura and Lott 2020 ). In contrast, regulation at the zygotic stage can be gene or pathway specific and involve transcription only in a spatially localized subset of cells ( Jäckle et al 1986 ; Johnston and Nüsslein-Volhard 1992 ).…”

“…These binding sites have also been associated with housekeeping genes ( Zabidi et al 2015 ), and the pool of maternal transcripts is enriched with housekeeping genes ( Liu et al 2014 ). However, maternal genes that are not housekeeping genes are even more highly enriched for these binding sites ( Omura and Lott 2020 ), thus the involvement of insulators or other chromatin regulators in maternal regulation is unlikely solely due to the inclusion of housekeeping genes among maternal genes. Transcript abundance data from our study indicates that Dref , BEAF-32 , and M1BP are differentially maternally deposited in several between-species comparisons (Figure S4), although, in certain crosses, hybrid reads mapped in a biased way to Dref , BEAF-32 , and M1BP , and thus they were excluded from our regulatory analysis.…”

“…We used the Differential Enrichment mode in MEME ( Bailey and Elkan 1994 ) as well as the findMotifs.pl script in HOMER ( Heinz et al 2010 ) to identify overrepresented motifs in the regions 500 bp upstream of the annotated starting location for genes changing in regulation or with conserved regulation between species in every set of comparisons at stage 2. We utilized a 500 bp region as this was empirically determined to give the highest enrichment of signal for motifs in target genes relative to background [see Omura and Lott (2020) for more information]. In MEME, we used options to find motifs with any number of repetitions and a motif width of 8–12.…”