Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

SCHOR, IGNACIO E.; BUSSOTTI, GIOVANNI; MALE?, MATILDA; FORNERIS, MATTIA; VIALES, REBECCA R.; ENRIGHT, ANTON J.; FURLONG, EILEEN E.M.

CURRENT BIOLOGY

CELL PRESS

Año: 2018 vol. 28 p. 3547 - 3561

0960-9822

Long non-coding RNAs (lncRNAs) can often function in the regulation of gene expression during development; however, their generality as essential regulators in developmental processes and organismal phenotypes remains unclear. Here, we performed a tailored investigation of lncRNA expression and function during Drosophila embryogenesis, interrogating multiple stages, tissue specificity, nuclear localization, and genetic backgrounds. Our results almost double the number of annotated lncRNAs expressed at these embryonic stages. lncRNA levels are generally positively correlated with those of their neighboring genes, with little evidence of transcriptional interference. Using fluorescent in situ hybridization, we report the spatiotemporal expression of 15 new lncRNAs, revealing very dynamic tissue-specific patterns. Despite this, deletion of selected lncRNA genes had no obvious developmental defects or effects on viability under standard and stressed conditions. However, two lncRNA deletions resulted in modest expression changes of a small number of genes, suggesting that they fine-tune expression of non-essential genes. Several lncRNAs have strain-specific expression, indicating that they are not fixed within the population. This intra-species variation across genetic backgrounds may thereby be a useful tool to distinguish rapidly evolving lncRNAs with as yet non-essential roles. Schor et al. identify hundreds of new lncRNAs expressed at specific embryonic stages and in mesoderm. Many have very specific spatiotemporal expression. Deletion of 3 lncRNAs are viable with no obvious phenotypes, even when stressed. Many lncRNAs have strain-specific expression, highlighting how sequence variation leads to intergenic transcription.