The scientific and technical breakthrough of the draft sequence of the human genome in 2001 and the advent of genome wide technologies have dramatically altered our view of genome organization and function. We know now that more than 70% of the human genome is transcribed, although only 2% encode proteins. Within this huge percentage of supposedly “garbage” transcripts, thousands of long non-coding RNAs (lncRNAs) have been described. lncRNAs are characterized by their extensive regulation during development, particularly in the central nervous system (CNS), where some have been shown to affect cognitive and locomotor functions. Drosophila melanogaster is an ideal model for studying the role of lncRNAs during development and has been used successfully to investigate the molecular and cellular basis of neurodegenerative disorders. To address the relevance and functions of lncRNAs during CNS development, we plan to identify and characterize lncRNAs in Drosophila neurons by applying several innovative, robust, and genome wide technologies. Taking advantage of the power of Drosophila genetics, we will study the in vivo roles of selected CNS lncRNAs, at both the morphological and functional levels, in two mushroom body (MB) neuron paradigms. Using the most modern instruments and methods available, we will explore the neuronal functions of candidate CNS lncRNAs by their genetic knock-down and phenotypic analysis in vivo, analysis of their subcellular localization, trafficking and identification of their protein partners.To date, no systematic investigation of lncRNAs during CNS development addressing their expression patterns, localization and in vivo function in a living organism has been reported. Hence this interdisciplinary project, which will shed important insight into the biological functions of lncRNAs in the CNS, is both ambitious and novel.