Drosophila melanogaster embryonic development RAMPAGE time series (Biological replicate #2)

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. Overall design: 23 Samples of Drosophila melanogaster多细胞生物的发育在很大程度上由转录调控程序决定，这些程序协同调控数千个编码蛋白基因与非编码基因的表达。为解析指定这些调控程序的基因组调控密码，并全局探究非编码转录的发育相关性，我们对5个果蝇（Drosophila）物种的全基因组启动子活性在整个胚胎发育过程中进行了谱分析。我们发现，以往普遍认为不具备显著调控功能的核心启动子（core promoter），实则在全基因组范围内对基因表达的发育时序施加了广泛限制。我们提出了发育过程中转录调控的层级模型：核心启动子通过限定自身可接收调控输入的转录因子范围，为基因表达划定宽泛的表达许可窗口。这种双层调控机制全局协调发育基因的表达，其调控规模远超当前我们对个体发生（ontogenesis）的认知。事实上，非编码转录本的丰度远超以往报道，胚胎发育过程中共表达有约4000种长非编码RNA（long noncoding RNA）。其中超过1500种在黑腹果蝇亚组（melanogaster subgroup）中具有功能保守性，另有数百种受到强烈的纯化选择。总而言之，本研究提出了发育过程中转录调控的层级模型，并揭示了非编码转录在动物发育中的核心作用。实验设计概述：共包含23个黑腹果蝇（Drosophila melanogaster）样本。