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

Abstract

Multicellular development is driven by regulatory programs that orchestrate the transcription of protein-coding and noncoding genes. To decipher this genomic regulatory code, and to investigate the developmental relevance of noncoding transcription, we compared genome-wide promoter activity throughout embryogenesis in 5 Drosophila species. Core promoters, generally not thought to play a significant regulatory role, in fact impart restrictions on the developmental timing of gene expression on a global scale. We propose a hierarchical regulatory model in which core promoters define broad windows of opportunity for expression, by defining a range of transcription factors from which they can receive regulatory inputs. This two-tiered mechanism globally orchestrates developmental gene expression, including extremely widespread noncoding transcription. The sequence and expression specificity of noncoding RNA promoters are evolutionarily conserved, implying biological relevance. Overall, this work introduces a hierarchical model for developmental gene regulation, and reveals a major role for noncoding transcription in animal development.

Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection

“…Besides, our virus-infected transcriptome analysis also revealed that, similar to other well-studied organisms (Batut and Gingeras, 2017;Engreitz et al, 2016), Ae. albopictus lncRNAs presumably possess their own regulatory elements that specifically govern their expression in response to viralinfection, independent of the neighboring protein-coding genes.…”

Insights into the Functions of LncRNAs in Drosophila

“…At this critical moment in the initial stage of metamorphosis, the considerable upregulation of lncRNAs signified that lncRNA enrichment in development could be important for transformation and organogenesis [60]. Another study demonstrated that the sequence and expression specificity of non-coding RNA promoters were evolutionarily conserved in five Drosophila strains and that a substantial proportion of lncRNAs might be related to embryonic development [61]. RNA-seq of three different parts among multiple developmental stages of embryos suggested that: (1) most lncRNAs had dynamic expression patterns; (2) a set of lncRNAs showed significant Gene Ontology (GO) term enrichments, which were mainly related to segment specification; and (3) the majority of the 30 tested lncRNAs gave a specific and even restricted expression atlas [62].…”

Two promoters integrate multiple enhancer inputs to drive wild-typeknirpsexpression in theD. melanogasterembryo

“…Expression data for the two kni promoters is shown, with RAMPAGE data (P. J. Batut & Gingeras, 2017) in (B) and RNA-seq data (Lott et al, 2011) in (C) ; the time period corresponding to the blastoderm stage is highlighted in gray. Based on these two sets of data, the two kni promoters are both used during nuclear cycle 14 though which one is more active is less clear.…”

“…They also differ in the “sharpness” of their region of transcription initiation (shown between the brackets), with promoter 1 (124bp) being significantly broader than promoter 2 (3bp) based on RAMPAGE tag data (P. J. Batut & Gingeras, 2017).…”