title: Digital expression profiling of the compartmentalized translatome of Purkinje neurons.
abstract: Underlying the complexity of the mammalian brain is its network of neuronal connections, but also the molecular networks of signaling pathways, protein interactions, and regulated gene expression within each individual neuron. The diversity and complexity of the spatially intermingled neurons pose a serious challenge to the identification and quantification of single neuron components. To address this challenge, we present a novel approach for the study of the ribosome-associated transcriptome-the translatome-from selected subcellular domains of specific neurons, and apply it to the Purkinje cells (PCs) in the rat cerebellum. We combined microdissection, translating ribosome affinity purification (TRAP) in nontransgenic animals, and quantitative nanoCAGE sequencing to obtain a snapshot of RNAs bound to cytoplasmic or rough endoplasmic reticulum (rER)-associated ribosomes in the PC and its dendrites. This allowed us to discover novel markers of PCs, to determine structural aspects of genes, to find hitherto uncharacterized transcripts, and to quantify biophysically relevant genes of membrane proteins controlling ion homeostasis and neuronal electrical activities.
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Anton
authors.initials: A
authors.lastname: Kratz
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan.
authors.forename: Pascal
authors.initials: P
authors.lastname: Beguin
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan.
authors.forename: Megumi
authors.initials: M
authors.lastname: Kaneko
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan.
authors.forename: Takahiko
authors.initials: T
authors.lastname: Chimura
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Suzuki
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan.
authors.forename: Atsuko
authors.initials: A
authors.lastname: Matsunaga
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Sachi
authors.initials: S
authors.lastname: Kato
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan.
authors.forename: Réjan
authors.initials: R
authors.lastname: Vigot
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan;
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.affiliation: RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan; plessy@riken.jp thomas.launey@riken.jp.
authors.forename: Charles
authors.initials: C
authors.lastname: Plessy
authors.affiliation: RIKEN Brain Science Institute, Launey Research Unit, Wako, Saitama, 351-0198 Japan plessy@riken.jp thomas.launey@riken.jp.
authors.forename: Thomas
authors.initials: T
authors.lastname: Launey
mesh_terms: D000818:Animals; D001665:Binding Sites; D002874:Chromosome Mapping; D016000:Cluster Analysis; D003593:Cytoplasm / Q000378:metabolism; D003712:Dendrites / Q000378:metabolism; D018870:Endoplasmic Reticulum, Rough / Q000378:metabolism; D020869:Gene Expression Profiling; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D011689:Purkinje Cells / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D051381:Rats; D012270:Ribosomes / Q000502:physiology; D059467:Transcriptome
chemical_list: D022661:RNA, Untranslated