title: Nuclear RNA-seq of single neurons reveals molecular signatures of activation.
abstract: 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.
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lacar
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Sara B
authors.initials: SB
authors.lastname: Linker
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Baptiste N
authors.initials: BN
authors.lastname: Jaeger
authors.affiliation: J. Craig Venter Institute, La Jolla, California 92037, USA.
authors.forename: Suguna R
authors.initials: SR
authors.lastname: Krishnaswami
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Jerika J
authors.initials: JJ
authors.lastname: Barron
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Martijn J E
authors.initials: MJE
authors.lastname: Kelder
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Parylak
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Apuã C M
authors.initials: ACM
authors.lastname: Paquola
authors.affiliation: J. Craig Venter Institute, La Jolla, California 92037, USA.
authors.forename: Pratap
authors.initials: P
authors.lastname: Venepally
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Carolyn
authors.initials: C
authors.lastname: O'Connor
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Conor
authors.initials: C
authors.lastname: Fitzpatrick
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Erwin
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Jonathan Y
authors.initials: JY
authors.lastname: Hsu
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: David
authors.initials: D
authors.lastname: Husband
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: McConnell
authors.affiliation: J. Craig Venter Institute, La Jolla, California 92037, USA.
authors.forename: Roger
authors.initials: R
authors.lastname: Lasken
authors.affiliation: Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
authors.forename: Fred H
authors.initials: FH
authors.lastname: Gage
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics; D003598:Cytoskeletal Proteins / Q000235:genetics / Q000378:metabolism; D018891:Dentate Gyrus / Q000166:cytology / Q000378:metabolism; D051766:Early Growth Response Protein 1 / Q000235:genetics / Q000378:metabolism; D063990:Gene Ontology; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D017874:Immediate-Early Proteins / Q000235:genetics / Q000378:metabolism; D007150:Immunohistochemistry; D008810:Mice, Inbred C57BL; D008822:Mice, Transgenic; D018613:Microscopy, Confocal; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D009474:Neurons / Q000378:metabolism*; D016760:Proto-Oncogene Proteins c-fos / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D059467:Transcriptome; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism; D000098551:Prospero-Related Homeobox 1 Protein
chemical_list: D003598:Cytoskeletal Proteins; D051766:Early Growth Response Protein 1; D018398:Homeodomain Proteins; D017874:Immediate-Early Proteins; D009419:Nerve Tissue Proteins; D016760:Proto-Oncogene Proteins c-fos; D025521:Tumor Suppressor Proteins; C092069:activity regulated cytoskeletal-associated protein; D000098551:Prospero-Related Homeobox 1 Protein