Nuclear RNA-seq of single neurons reveals molecular signatures of activation

Benjamin Lacar; Sara B Linker; Baptiste N Jaeger; Suguna R Krishnaswami; Jerika J Barron; Martijn J E Kelder; Sarah L Parylak; Apuã 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

doi:10.1038/ncomms11022

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

Nat Commun. 2016 Apr 19:7:11022. doi: 10.1038/ncomms11022.

Authors

Benjamin Lacar¹, Sara B Linker¹, Baptiste N Jaeger¹, Suguna R Krishnaswami², Jerika J Barron¹, Martijn J E Kelder¹, Sarah L Parylak¹, Apuã C M Paquola¹, Pratap Venepally², Mark Novotny¹, Carolyn O'Connor¹, Conor Fitzpatrick¹, Jennifer A Erwin¹, Jonathan Y Hsu¹, David Husband¹, Michael J McConnell³, Roger Lasken², Fred H Gage¹

Affiliations

¹ Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037-1002, USA.
² J. Craig Venter Institute, La Jolla, California 92037, USA.
³ Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cell Nucleus / genetics
Cytoskeletal Proteins / genetics
Cytoskeletal Proteins / metabolism
Dentate Gyrus / cytology
Dentate Gyrus / metabolism
Early Growth Response Protein 1 / genetics
Early Growth Response Protein 1 / metabolism
Gene Ontology
Homeodomain Proteins / genetics
Homeodomain Proteins / metabolism
Immediate-Early Proteins / genetics
Immediate-Early Proteins / metabolism
Immunohistochemistry
Mice, Inbred C57BL
Mice, Transgenic
Microscopy, Confocal
Nerve Tissue Proteins / genetics
Nerve Tissue Proteins / metabolism
Neurons / metabolism*
Prospero-Related Homeobox 1 Protein
Proto-Oncogene Proteins c-fos / genetics
Proto-Oncogene Proteins c-fos / metabolism
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, RNA / methods*
Single-Cell Analysis / methods*
Transcriptome*
Tumor Suppressor Proteins / genetics
Tumor Suppressor Proteins / metabolism

Substances

Cytoskeletal Proteins
Early Growth Response Protein 1
Homeodomain Proteins
Immediate-Early Proteins
Nerve Tissue Proteins
Proto-Oncogene Proteins c-fos
Tumor Suppressor Proteins
activity regulated cytoskeletal-associated protein
Prospero-Related Homeobox 1 Protein

Associated data

GEO/GSE77067

Abstract

Publication types

MeSH terms

Substances

Associated data

Grants and funding