Aliperti, Vincenza (2018) IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CODING GENES AND LONG NON-CODING RNAS INVOLVED IN NEURONAL DEVELOPMENT. [Tesi di dottorato]

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Abstract

Neuronal differentiation is a complex process characterized by different cellular events. It is finely regulated by numerous transcription factors, many of which have been identified while others remain unknown. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression, with an essential role in cell differentiation. Therefore, the identification and characterization of these transcripts and the functional relationships between mRNA and lncRNA are fundamental to the understanding the complex transcriptional processes underlying gene regulation. In this regard, an essential molecule for neuronal development, the neurotrophin BDNF (Brain-Derived Neurotrophic Factor), is known for its action in post-transcriptional regulation, while little is known about the transcriptional programs it triggers and through which it influences the development and survival of neurons. The results presented in this thesis concerns the identification of several Immediate Early Genes (IEGs), belonging to both coding and non-coding that, engaged by BDNF, can play a fundamental role in the biology of this neurotrophin. Among coding genes, the involvement of the transcription factor EGR1 (Early growth response protein 1) in neuronal differentiation was investigated. Taking advantage of genome editing techniques (CRISPR-Cas9) and the SH-SY5Y cell line as a human neuronal model, I showed that the knockout cells for EGR1 are unable to differentiate, underlining an essential role of the transcriptional programs regulated by EGR1 in the survival of neurons. Furthermore, I identified a new alternative splicing isoform for EGR1 likely involved in neuronal differentiation. The preliminary results suggested that this isoform may act as a dominant negative of the canonical isoform, contributing to a fine regulation of its effect on transcriptional regulation. In the final part of my thesis, I focused my efforts on a primary characterization of the most differentially expressed lncRNA under BFNF stimulation, the LINC00473 gene. I provided evidence that this gene may encode for a little protein highly conserved in primate species. Functional analysis by the use of a KO cell line generated by CRISPR/Cas9 showed that the putative protein affected the transcript level of the IEGs with a relevant impact on the regulation of gene expression.

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