Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing
Summary
We developed a new viral affinity purification strategy, Cre-Specific Nuclear Anchored Independent Labeling (cSNAIL), to isolate Cre recombinase-expressing (Cre+) nuclei from the adult mouse brain. cSNAIL is an AAV that delivers a modified version of the nuclear-anchored protein tag developed for INTACT nuclei isolation (Deal & Henikoff, Dev Cell. 2010. 18:1030-1040; Mo et al., Neuron. 2015. 86(6):1369-1384). Applying cSNAIL technology in Pvalb-2A-Cre mice, we performed targeted assessment of the cell type-specific transcriptomic and epigenetic effects of dopamine depletion on parvalbumin-expressing (PV+) neurons and PV- nuclei. We recovered signatures of oxidative stress response involving Hif2a signaling that was specific to external globus pallidus (GPe) PV+ neurons, a consequence of dopamine depletion that may have theraputic implications for Parkinson's disease.
Overall design
We collected RNA-seq and ATAC-seq from cSNAIL-isolated populations of PV neurons and remaining cells in the mouse isocortex, striatum, and GPe. The subjects were either dopamine depleted via acute, bilateral 6-hydroxydopamine (6-OHDA) lesion, or healthy controls that recieved a sham surgery. Both sexes were represented in both treatment groups.
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