The landscape of the long non-coding RNAs in developing mouse retinas

BackgroundThe long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available.ResultsHerein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways.ConclusionsIn summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.

Automated summary

Based on established gene models and ab initio prediction, this study characterized 4,523 lncRNA genes in developing mouse retinas, providing the most comprehensive collection of retinal lncRNAs to date. These lncRNAs were found to be highly spatiotemporal specific in expression and played essential roles in regulating retinal genesis and function. The expression of certain lncRNAs was found to be implicated in the regulation of retinal neuron differentiation and development through specific pathways.