title: Comparison of parallel high-throughput RNA sequencing between knockout of TDP-43 and its overexpression reveals primarily nonreciprocal and nonoverlapping gene expression changes in the central nervous system of Drosophila.
abstract: The human Tar-DNA binding protein, TDP-43, is associated with amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. TDP-43 contains two conserved RNA-binding motifs and has documented roles in RNA metabolism, including pre-mRNA splicing and repression of transcription. Here, using Drosophila melanogaster as a model, we generated loss-of-function and overexpression genotypes of Tar-DNA binding protein homolog (TBPH) to study their effect on the transcriptome of the central nervous system (CNS). By using massively parallel sequencing methods (RNA-seq) to profile the CNS, we find that loss of TBPH results in widespread gene activation and altered splicing, much of which are reversed by rescue of TBPH expression. Conversely, TBPH overexpression results in decreased gene expression. Although previous studies implicated both absence and mis-expression of TDP-43 in ALS, our data exhibit little overlap in the gene expression between them, suggesting that the bulk of genes affected by TBPH loss-of-function and overexpression are different. In combination with computational approaches to identify likely TBPH targets and orthologs of previously identified vertebrate TDP-43 targets, we provide a comprehensive analysis of enriched gene ontologies. Our data suggest that TDP-43 plays a role in synaptic transmission, synaptic release, and endocytosis. We also uncovered a potential novel regulation of the Wnt and BMP pathways, many of whose targets appear to be conserved.
authors.affiliation: Department of Integrative Biosciences, Oregon Health & Science University, Portland, Oregon 97239, USA.
authors.forename: Dennis J
authors.initials: DJ
authors.lastname: Hazelett
authors.forename: Jer-Cherng
authors.initials: JC
authors.lastname: Chang
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Lakeland
authors.forename: David B
authors.initials: DB
authors.lastname: Morton
mesh_terms: D000818:Animals; D001665:Binding Sites; D002490:Central Nervous System / Q000378:metabolism; D016000:Cluster Analysis; D004268:DNA-Binding Proteins / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism; D029721:Drosophila Proteins / Q000172:deficiency / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics*; D005786:Gene Expression Regulation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D012326:RNA Splicing
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins