title: Analysis of area-specific expression patterns of RORbeta, ER81 and Nurr1 mRNAs in rat neocortex by double in situ hybridization and cortical box method.
abstract: BACKGROUND
  The mammalian neocortex is subdivided into many areas, each of which exhibits distinctive lamina architecture. To investigate such area differences in detail, we chose three genes for comparative analyses, namely, RORbeta, ER81 and Nurr1, mRNAs of which have been reported to be mainly expressed in layers 4, 5 and 6, respectively. To analyze their qualitative and quantitative coexpression profiles in the rat neocortex, we used double in situ hybridization (ISH) histochemistry and cortical box method which we previously developed to integrate the data of different staining and individuals in a standard three-dimensional space.
  
  
  RESULTS
  Our new approach resulted in three main observations. First, the three genes showed unique area distribution patterns that are mostly complementary to one another. The patterns revealed by cortical box method matched well with the cytoarchitectonic areas defined by Nissl staining. Second, at single cell level, RORbeta and ER81 mRNAs were coexpressed in a subpopulation of layer 5 neurons, whereas Nurr1 and ER81 mRNAs were not colocalized. Third, principal component analysis showed that the order of hierarchical processing in the cortex correlates well with the expression profiles of these three genes. Based on this analysis, the dysgranular zone (DZ) in the somatosensory area was considered to exhibit a profile of a higher order area, which is consistent with previous proposal.
  
  
  CONCLUSIONS
  The tight relationship between the expression of the three layer specific genes and functional areas were revealed, demonstrating the usefulness of cortical box method in the study on the cerebral cortex. In particular, it allowed us to perform statistical evaluation and pattern matching, which would become important in interpreting the ever-increasing data of gene expression in the cortex.
authors.affiliation: Division of Brain Biology, National Institute for Basic Biology, Okazaki, Japan.
authors.forename: Junya
authors.initials: J
authors.lastname: Hirokawa
authors.forename: Akiya
authors.initials: A
authors.lastname: Watakabe
authors.forename: Sonoko
authors.initials: S
authors.lastname: Ohsawa
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Yamamori
mesh_terms: D000818:Animals; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000096:biosynthesis*; D005786:Gene Expression Regulation; D007091:Image Processing, Computer-Assisted; D017403:In Situ Hybridization; D008297:Male; D051379:Mice; D019579:Neocortex / Q000378:metabolism*; D057095:Nuclear Receptor Subfamily 1, Group F, Member 2; D057126:Nuclear Receptor Subfamily 4, Group A, Member 2; D012333:RNA, Messenger / Q000378:metabolism; D051381:Rats; D018160:Receptors, Cytoplasmic and Nuclear / Q000096:biosynthesis* / Q000235:genetics; D014018:Tissue Distribution; D015534:Trans-Activators / Q000096:biosynthesis*; D014157:Transcription Factors / Q000096:biosynthesis*
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D004268:DNA-Binding Proteins; C510952:ETV1 protein, rat; C539883:Nr4a2 protein, mouse; C539884:Nr4a2 protein, rat; D057095:Nuclear Receptor Subfamily 1, Group F, Member 2; D057126:Nuclear Receptor Subfamily 4, Group A, Member 2; D012333:RNA, Messenger; D018160:Receptors, Cytoplasmic and Nuclear; C539741:Rorb protein, mouse; D015534:Trans-Activators; D014157:Transcription Factors