  The time required to transcribe genes with long primary transcripts may limit
their ability to be expressed in cells with short mitotic cycles, a phenomenon
termed intron delay. As such short cycles are a hallmark of the earliest stages
of insect development, we used Drosophila developmental timecourse expression
data to test whether intron delay affects gene expression genome-wide, and to
determine its consequences for the evolution of gene structure. We find that
long zygotically expressed, but not maternally deposited, genes show
substantial delay in expression relative to their shorter counterparts and that
this delay persists over a substantial portion of the ~24 hours of
embryogenesis. Patterns of RNA-seq coverage from the 5' and 3' ends of
transcripts show that this delay is consistent with their inability to
terminate transcription, but not with transcriptional initiation-based
regulatory control. Highly expressed zygotic genes are subject to purifying
selection to maintain compact transcribed regions, allowing conservation of
embryonic expression patterns across the Drosophila phylogeny. We propose that
intron delay is an underappreciated physical mechanism affecting both patterns
of expression as well as gene structure of many genes across Drosophila.
