Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics

The developing neocortex in the mammalian brain is composed of multiple cell types including apical progenitors (AP), basal progenitors (BP), and neurons that populate three different layers, the ventricular zone (VZ), the subventricular zone (SVZ), and the cortical plate (CP). Despite recent advances, the diversity of the existing cell populations including those which are differentiating and mature, their biogenesis and the underlying gene regulatory mechanisms remain poorly known. Recent studies have taken advantage of the rapidly emerging single-cell technologies to decode the heterogeneity of cell populations at the transcriptome level during cortical development and their molecular details. Here we review these studies and provide an overview of the steps in single-cell transcriptomics including both experimental and computational analysis. We also discuss how single-cell genomics holds a big potential in future for brain research and discuss its possible applications and biological insights that can be achieved from these approaches. We conclude this review by discussing the current challenges in the implementation of single-cell techniques toward a comprehensive understanding of the genetic and epigenetic mechanisms underlying neocortex development.