Gene expression profiling of shRNA transduced rat hippocampal neurons
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ABSTRACT:
PROVIDER: PRJNA642132 | ENA |
REPOSITORIES: ENA
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Project description:Sirtuin 6 (SIRT6), a member of the sirtuin family, acts as nicotinamide adenine dinucleotide-dependent protein deacetylase, mono-adenosine diphosphate-ribosyltransferase, and fatty acid deacylase and plays critical roles in inflammation, aging, glycolysis, and DNA repair. Accumulating evidence has suggested that SIRT6 is involved in brain functions such as neuronal differentiation, neurogenesis, and learning and memory. However, the precise molecular roles of SIRT6 during neuronal circuit formation are not well understood. In this study, we attemped to elucidate the molecular roles of SIRT6 on neurite development using a primary culture of hippocampal neurons. We observed that SIRT6 was abundantly localized in the nucleus, and its expression was markedly increased during neurite outgrowth and synaptogenesis. Using shRNA-mediated SIRT6 knockdown, we showed that the dendritic length and number of dendrite branches were significantly reduced in SIRT6 knockdown neurons. Microarray and subsequent gene ontology analysis revealed that reducing SIRT6 caused the downregulation of immediate early genes (IEGs) and alteration of several biological processes including MAPK (ERK1/2) signaling. We found that nuclear accumulation of phosphorylated ERK1/2 was significantly reduced in SIRT6 knockdown neurons. Overexpression of SIRT6 promoted dendritic length and branching, but the mutants lacking deacetylase activity had no significant effect on the dendritic morphology. Collectively, the presented findings reveal a role of SIRT6 in dendrite morphogenesis and suggest that SIRT6 may act as an important regulator of the ERK1/2 signaling pathway that mediates IEG expression, which leads to dendritic development.
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Project description:We analyzed the binding profiles of MEF2D, a member of MEF2 family transcription factors, in rat hippocampal neurons. Keywords: ChIP-chip We used custom-designed rat genome tiling array manufactured by Nimblegen Systems, Inc . This array contains probes that represent the following rat genomic regions: 182 genes identified by mRNA profiling experiments, 86 genes whose expression was decreased by both KCl-mediated depolarization and MEF2 RNAi, and 40 control genes whose expression was not altered by MEF2 RNAi or MEF2-VP16-ER. The array not only covers the entire gene regions but also contains probes that correspond to the 40 kb 5â²and 3â² to each gene. Repeatmasking was conducted by Nimblegen to ensure that repetitive elements were not tiled on the microarray. Probe length and spacing between the probes were 50-75mer and 50 bp, respectively.
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