The influence of tropomyosin gene overexpression on neuron-specific transcriptome patterns

Abstract

Actin cytoskeleton has been implicated in a diversity of cellular functions and its role in neuronal morphology has been intensively studied. In non-skeletal cells, distinct populations of actin filaments in different subcellular compartments are characterised by the specific isoforms of actin-associated tropomyosin. To investigate the effect of different tropomyosin isoforms on neuron physiology at the transcriptomic level, transcriptome sequence data from transgenic Tp8 mice overexpressing human cytoskeletal tropomyosin TM5NM1 and rat neuroblastoma cell line B35 cells overexpressing human cytoskeletal tropomyosin TM1 and TM5NM1, mouse cytoskeletal tropomyosin TmBr3 and Tm4 were analysed using a Galaxy bioinformatics analysis pipeline consisted of TopHat, Cufflinks, and Cuffdiff, followed by pathway analysis using DAVID. Results showed that in vivo and in vitro TM5NM1 overexpression resulted in different numbers of differentially expressed genes and isoforms as well as enriched gene ontology terms. For instance, the expression of transthyretin (FC = 23.54, p-value = 0.008) was significantly up-regulated in the transgenic Tp8 mice but not in the B35 cell lines. While PR Domain Containing 5 gene was silenced in all transfected B35 cells, its differential expression in Tp8 mice was not detected. In Tp8 mice but not B35 cells GO terms such as GO:0002376 immune system process and GO:0048002 antigen processing and presentation of peptide antigen were found enriched. GO terms such as GO:000904 cell morphogenesis involved in differentiation and GO:0048667 cell morphogenesis involved in neuron differentiation were exclusively enriched in B35 cells. In contrast, pathway analysis of rat neuronal cell line revealed mostly similar transcriptome patterns as a result of overexpression of TM1, TmBr3, Tm4, and TM5NM1 isoforms of tropomyosin. This is the first time the effects of overexpression of distinct tropomyosin isoforms on gene expression profiles been investigated using next-generation sequencing technology.