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Nuclear RNA-seq of single neurons reveals molecular signatures of activation (single nuclei)
Benjamin Lacar, Sara B Linker, Baptiste N Jaeger, Suguna R Krishnaswami, Jerika J Barron, Martijn J E Kelder, Sarah L Parylak, Apua C M Paquola, Pratap Venepally, Mark Novotny, Carolyn O Connor, Conor Fitzpatrick, Jennifer A Erwin, Jonathan Y Hsu, David Husband, Michael J McConnell, Roger Lasken, Fred H Gage
Single-cell sequencing methods have emerged as powerful tools for identification of
heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a
pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo.