title: Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq.
abstract: To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate. The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities. Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance. Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3' untranslated regions (3' UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to elucidate the complex transcriptional landscape in two neuronal populations.
authors.affiliation: The Miami Project to Cure Paralysis, Miller School of Medicine, University of Miami, Miami, Florida, United States of America.
authors.forename: Jessica K
authors.initials: JK
authors.lastname: Lerch
authors.forename: Frank
authors.initials: F
authors.lastname: Kuo
authors.forename: Dario
authors.initials: D
authors.lastname: Motti
authors.forename: Richard
authors.initials: R
authors.lastname: Morris
authors.forename: John L
authors.initials: JL
authors.lastname: Bixby
authors.forename: Vance P
authors.initials: VP
authors.lastname: Lemmon
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D002478:Cells, Cultured; D002490:Central Nervous System / Q000166:cytology / Q000378:metabolism; D002531:Cerebellum / Q000166:cytology / Q000378:metabolism; D016000:Cluster Analysis; D005727:Ganglia, Spinal / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016015:Logistic Models; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000235:genetics; D009474:Neurons / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D017933:Peripheral Nervous System / Q000166:cytology / Q000378:metabolism; D020033:Protein Isoforms / Q000235:genetics; D011984:Sensory Receptor Cells / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D020121:5' Untranslated Regions; D035683:MicroRNAs; D020033:Protein Isoforms; D014157:Transcription Factors