Functional consequences of heterogeneity in transcriptional initiation

Abstract

The eukaryotic core promoter is an essential regulatory part of the genome. Its sequence dictates the transcriptional output from any specific gene and it can alter the output in response to external and internal stimuli. The transcriptional start site (TSS), where RNA polymerases bind and initiate transcription, is at the base of the core promoter, and dynamic mapping of initiation sites can reveal how the cell utilises alternative core promoter features. I first map core promoters in Drosophila development by using a low-input, single-nucleotide resolution mapping protocol for identification of TSSs, SLIC-CAGE. The maternal and zygotic genomes are mostly guided by distinct codes of initiation, with maternal genes being dependant on nucleosome positioning signals and zygotic genes on precisely-positioned motifs. Despite specific initiation rules used by the maternal and zygotic genomes, I find no evidence for overlapping codes used in the same promoter, a feature that has been demonstrated to be conserved in vertebrate development. However, I also demonstrate that there is evidence of alternative use of YC and YR initiation in promoters harbouring both. One of the most striking features of core promoters revealed by accurate TSS mapping is the two modes of initiation. Sharp initiation is characterised by a single TSS usage, while broad initiation refers to multiple, closely-spaced TSSs. Much less is known about how transcripts arising from broad initiation differ in their downstream processing. I demonstrate that individual TSSs have distinct translational properties by combining SLIC-CAGE with polysome fractionated RNA. This is particularly striking in YC/YR dual-initiation promoters, which might explain their high prevalence in the genome. Finally, I demonstrate differential translational dynamics of zygotic RNAs initiated at specific core promoter motifs in the zygote, as well as RNAs expressed in both maternal and zygotic genomes. Again, YC and YR initiation in the zygotic genome show distinct properties, with high expression but low translation of YC promoters in the zygote, suggesting that the high transcription compensates for the inefficient translation.