Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal

Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11836-41. doi: 10.1073/pnas.1209647109. Epub 2012 Jul 2.


The expansion of the neocortex during mammalian brain evolution results primarily from an increase in neural progenitor cell divisions in its two principal germinal zones during development, the ventricular zone (VZ) and the subventricular zone (SVZ). Using mRNA sequencing, we analyzed the transcriptomes of fetal human and embryonic mouse VZ, SVZ, and cortical plate. In mouse, the transcriptome of the SVZ was more similar to that of the cortical plate than that of the VZ, whereas in human the opposite was the case, with the inner and outer SVZ being highly related to each other despite their cytoarchitectonic differences. We describe sets of genes that are up- or down-regulated in each germinal zone. These data suggest that cell adhesion and cell-extracellular matrix interactions promote the proliferation and self-renewal of neural progenitors in the developing human neocortex. Notably, relevant extracellular matrix-associated genes include distinct sets of collagens, laminins, proteoglycans, and integrins, along with specific sets of growth factors and morphogens. Our data establish a basis for identifying novel cell-type markers and open up avenues to unravel the molecular basis of neocortex expansion during evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Analysis of Variance
  • Animals
  • Biological Evolution*
  • Cell Adhesion / physiology
  • Cluster Analysis
  • DNA Primers / genetics
  • Extracellular Matrix Proteins / metabolism*
  • Fetus / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental / genetics*
  • Humans
  • Immunohistochemistry
  • Laser Capture Microdissection
  • Mice
  • Neocortex / growth & development*
  • Neocortex / metabolism*
  • Polymerase Chain Reaction
  • Principal Component Analysis
  • RNA, Messenger / genetics
  • Sequence Analysis, RNA
  • Stem Cells / cytology*
  • Transcriptome / genetics*


  • DNA Primers
  • Extracellular Matrix Proteins
  • RNA, Messenger

Associated data

  • GEO/GSE38805