Identification of differentially expressed long non-coding RNAs in a model of neuron differentiation
Open Access
Author:
Khan, Fatima Mahmood
Area of Honors:
Biology
Degree:
Bachelor of Science
Document Type:
Thesis
Thesis Supervisors:
Nikolaos Tsotakos, Thesis Supervisor Sairam V Rudrabhatla, Thesis Honors Advisor
Keywords:
biology bioinformatics genetics RNA
Abstract:
Understanding the molecular mechanisms of the development of the nervous system is of paramount importance to fields of research ranging from embryology to the study of neurodegeneration. While the differentiation of neurons is relatively well understood, the role of long non-coding RNAs (lncRNA) in this process has not been elucidated. In the present study, publicly available transcriptomic data (Gene Expression Omnibus Series accession number GSE77383) from control- and retinoic acid (RA)-treated SH-SY5Y human neuroblastoma cells were analyzed to identify differentially expressed lncRNA. The raw data were quality tested, mapped to the human reference genome (GRCh38/hg38), and quantified to reveal differentially expressed (DE) genes. Of 3108 DE genes, 2291 were protein-coding and 817 were non-coding. Of these DE non-coding genes, 475 were upregulated and 342 were downregulated, and include lncRNAs, antisense and intronic transcripts, as well as transcripts coded from pseudogenes. Importantly, GNAS-AS1, an antisense transcript produced by an imprinted gene was the most upregulated lncRNA in the differentiated cells. GNAS is responsible for the synthesis of the alpha subunit of the Gs protein, a GTPase that is critical to neuron signaling. Other ncRNAs, such as FIRRE and the miRNA host gene miR100HG, were also upregulated. The significance of the differential expression of these molecules will be explored in future studies.
