title: Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex.
abstract: The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Sofia
authors.initials: S
authors.lastname: Fertuzinhos
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Mingfeng
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA.
authors.forename: Yuka Imamura
authors.initials: YI
authors.lastname: Kawasawa
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Vedrana
authors.initials: V
authors.lastname: Ivic
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Franjic
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Darshani
authors.initials: D
authors.lastname: Singh
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Crair
authors.affiliation: Department of Neurobiology, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA. Electronic address: nenad.sestan@yale.edu.
authors.forename: Nenad
authors.initials: N
authors.lastname: Sestan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005260:Female; D053263:Gene Regulatory Networks; D008297:Male; D051379:Mice; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D019579:Neocortex / Q000378:metabolism / Q000502:physiology*; D012313:RNA / Q000096:biosynthesis* / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D022661:RNA, Untranslated; D012313:RNA