Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

• Published in: Cell reports (Cambridge) 2014-03, Vol.6 (5), p.938-950
• Main Authors: Fertuzinhos, Sofia, Li, Mingfeng, Kawasawa, Yuka Imamura, Ivic, Vedrana, Franjic, Daniel, Singh, Darshani, Crair, Michael, Šestan, Nenad
• Format: Article
• Language: English
• Subjects: Alternative Splicing; Animals; Female; Gene Regulatory Networks; Male; Mice; MicroRNAs - biosynthesis; MicroRNAs - genetics; Neocortex - metabolism; Neocortex - physiology; RNA - biosynthesis; RNA - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Untranslated - biosynthesis; RNA, Untranslated - genetics; Transcriptome
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2014.01.036

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. [Display omitted] •RNA-seq analysis of layers in the developing mouse neocortex•Analysis of coding and noncoding RNAs and putative miRNA-mRNA interactions•Identification of spatiotemporal expression patterns and transcript variants•Prediction of transcriptional overlap between distinct biological processes Šestan and colleagues now provide insight into transcriptional dynamics across layers of the developing and adult mouse cerebral neocortex using deep sequencing. The authors identify genes with distinct spatiotemporal expression patterns, distinct transcript variant expression, networks of coexpressed transcripts, and signature transcriptional trajectories and molecular candidates associated with distinct developmental events.