Conserved noncoding transcription and core promoter regulatory code in early Drosophila development

Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands of protein-coding and noncoding genes. To decipher the genomic regulatory code that specifies these programs, and to investigate globally the developmental relevance of noncoding transcription, we profiled genome-wide promoter activity throughout embryonic development in 5 Drosophila species. We show that core promoters, generally not thought to play a significant regulatory role, in fact impart broad restrictions on the developmental timing of gene expression on a genome-wide scale. We propose a hierarchical model of transcriptional regulation during development in which core promoters define broad windows of opportunity for expression, by defining a limited range of transcription factors from which they are able to receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including noncoding transcription on a scale that defies our current understanding of ontogenesis. Indeed, noncoding transcripts are far more prevalent than ever reported before, with [~]4,000 long noncoding RNAs expressed during embryogenesis. Over 1,500 are functionally conserved throughout the melanogaster subgroup, and hundreds are under strong purifying selection. Overall, this work introduces a hierarchical model for the developmental regulation of transcription, and reveals the central role of noncoding transcription in animal development.