A Resource for Transcriptomic Analysis in the Mouse Brain

Abstract

BackgroundThe transcriptome of the cerebral cortex is remarkably homogeneous, with variations being stronger between individuals than between areas. It is thought that due to the presence of many distinct cell types, differences within one cell population will be averaged with the noise from others. Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile.MethodologyWe have prepared a low-redundancy set of 16,209 full-length cDNA clones which represents the transcriptome of the mouse visual cortex in its coding and non-coding aspects. Using an independent tag-based approach, CAGE, we confirmed the cortical expression of 72% of the clones. Clones were amplified by PCR and spotted on glass slides, and we interrogated the microarrays with RNA from flow-sorted fluorescent cells from the cerebral cortex of parvalbumin-egfp transgenic mice.ConclusionsWe provide an annotated cDNA clone collection which is particularly suitable for transcriptomic analysis in the mouse brain. Spotting it on microarrays, we compared the transcriptome of EGFP positive and negative cells in a parvalbumin-egfp transgenic background and showed that more than 30% of clones are differentially expressed. Our clone collection will be a useful resource for the study of the transcriptome of single cell types in the cerebral cortex.

Choroid-Plexus-Derived Otx2 Homeoprotein Constrains Adult Cortical Plasticity

“…An important Otx2 target may be the enriched ATP metabolism in these fast-spiking cells (Plessy et al, 2008). Indeed, translation of nuclear-encoded mitochondrial mRNAs commonly follows homeoprotein capture by dopaminergic neurons or retinal ganglion cell growth cones (Alvarez-Fischer et al, 2011; Stettler et al, 2012; Yoon et al, 2012).…”

Clock Genes Control Cortical Critical Period Timing

“…Circadian rhythms have been shown to regulate redox homeostasis in the brain, and disruption of circadian genes causes neuronal oxidative damage (Musiek et al, 2013). Notably, fast-spiking PV-cells are highly metabolically active with a hallmark of abundant mitochondrial molecules (Plessy et al, 2008) and are particularly vulnerable to redox dysregulation as compared to other neuronal types, resulting in their enhanced oxidative stress and loss of PNNs (Cabungcal et al, 2013a,b). Direct cell autonomous redox dysregulation by deletion of the primary antioxidant (glutathione) synthetic enzyme ( Gclc ) only within PV-cells is sufficient to prolong critical period plasticity (Morishita et al, 2015).…”

Trehalose-Enhanced Isolation of Neuronal Sub-Types from Adult Mouse Brain

“…Our protocol produces an average of 1.21 pg of RNA per pyramidal neuron, and 3.7 pg of RNA per parvalbumin neuron. Using trehalose we processed parvalbumin neurons from adult mice and prepared libraries for expression profiling using cDNA arrays (30). More recently, using this protocol, we prepared libraries from parvalbumin and pyramidal neurons with the nanoCAGE protocol (31, 32), and the data from these libraries is being prepared for submission.…”