Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

Abstract

Cascades of zygotic gene expression pattern the anterior-posterior (AP) and dorsal-ventral (DV) axes of the early Drosophila embryo. Here, we used the global run-on sequencing assay (GRO-seq) to map the genome-wide RNA polymerase distribution during early Drosophila embryogenesis, thus providing insights into how genes are regulated. We identify widespread promoter-proximal pausing yet show that the presence of paused polymerase does not necessarily equate to direct regulation through pause release to productive elongation. Our data reveal that a subset of early Zelda-activated genes is regulated at the level of polymerase recruitment, whereas other Zelda target and axis patterning genes are predominantly regulated through pause release. In contrast to other signaling pathways, we found that bone morphogenetic protein (BMP) target genes are collectively more highly paused than BMP pathway components and show that BMP target gene expression requires the pause-inducing negative elongation factor (NELF) complex. Our data also suggest that polymerase pausing allows plasticity in gene activation throughout embryogenesis, as transiently repressed and transcriptionally silenced genes maintain and lose promoter polymerases, respectively. Finally, we provide evidence that the major effect of pausing is on the levels, rather than timing, of transcription. These data are discussed in terms of the efficiency of transcriptional activation required across cell populations during developmental time constraints.

Getting up to speed with transcription elongation by RNA polymerase II

“…However, it has been observed that patterns of Pol II density on promoters and gene bodies change in response to heat shock, hormones, and developmental signals 10,29,46–50 , indicating that the two prominent regulatory steps during early elongation are Pol II recruitment to the promoter and the release of paused Pol II to productive elongation (FIG. 1b).…”

Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways

“…In Drosophila , widespread Pol II pausing is first detected at the midblastula transition (MBT) stage [36]. GRO-seq assays have further revealed that ~55% of genes in early Drosophila embryos contain paused Pol II, and that pause release appears to be the dominant regulatory step for genes involved in anterior–posterior and dorsal-ventral axis patterning [75]. Using muscle development in Drosophila embryos as a model, Gaertner et al have shown that at different embryonic stages, a large number of inactive genes gradually acquire paused Pol II during the developmental time course and are poised for future gene activation by tissue-specific signals [37].…”

An interactive network of long non-coding RNAs facilitates the Drosophila sex determination decision

“…Activation of Sxl Pe is biphasic; the promoter is first set up in repressive chromatin which is the default or male state, after which it transitions to activation in females [24, 42]. The R1 region and R2 sense lncRNAs appear to favor this repressed state.…”