In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement has likely contributions to cognition. The cerebral cortex has a uniform laminar structure that historically has been divided into six layers. Sub-classes of pyramidal neurons and interneurons populate specific layers, each characterized by a different depth in the cortex with specific pattern of dendritic and axonal connectivity. However, analyzing these laminar differences is difficult and often suffers from subjectivity. We sequenced transcriptomes from layers 1-6b of the adult (P56) mouse primary somatosensory cortex to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells constituting these layers. 5,835 protein-coding genes and 66 noncoding RNA loci were found to be differentially expressed (‘patterned’) across the layers, based on a machine-learning model (naïve Bayes) approach. Layers 2-6b are each associated with specific functional and disease annotations that provide insights into their biological roles. This new resource greatly extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data sets, by providing quantitative expression levels, by being genome-wide, by including novel loci, and by identifying candidate alternatively spliced transcripts that are differentially expressed across layers.
King's College London (2011) Proc Physiol Soc 22, SA22
Research Symposium: Differential expression and functions of protein-coding and noncoding genes across mouse neocortical layers
T. Belgard1,3, A. C. Marques1, P. L. Oliver1, H. Abaan3, T. M. Sirey1,2, Z. Molnar2, E. H. Margulies3, C. P. Ponting1
1. Dept of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom. 2. Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom. 3. Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, United States.
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