Temporal controls over interareal cortical projection neuron fate diversity (connectID)

Interconnectivity between neocortical areas is critical for sensory integration and sensorimotor transformations. These functions are mediated by heterogeneous interareal cortical projection neurons (ICPN), which send axon branches to distinct cortical areas as well as to subcortical targets. Although ICPN are anatomically diverse, they are molecularly homogeneous and how the diversity of their anatomical and functional features emerge during development remains largely unknown. Here, we address this question by linking connectome and transcriptome in developing single ICPN of the mouse neocortex using a combination of MAPseq mapping (to identify single-neuron axonal projections) and single-cell RNA sequencing (to identify corresponding gene expression). Focusing on neurons of the primary somatosensory cortex (S1), we reveal a protracted unfolding of the molecular and functional differentiation of motor cortex-projecting (M) compared to secondary somatosensory cortex-projecting (S2) ICPN. We identify SOX11 as a temporally differentially expressed transcription factor in M vs. S2 ICPN. Postnatal manipulation of SOX11 expression level in S1 impaired sensorimotor connectivity and selectively disrupted exploratory behavior in freely moving mice. Together, our results reveal that within a single cortical area, different subtypes of ICPN have distinct postnatal molecular differentiation paces, which is then reflected in distinct circuit connectivities and functions. Dynamic differences in expression levels of largely generic set of genes, rather than fundamental differences in the identity of developmental genetic programs, may thus account for emergence of intra-type diversity in cortical neurons. Overall design: This record contains single cell transcriptomics data from 7 Fluidigm integrated fluidic circuits and 66 bulk RNA-seq from the same 11 mouse cortex. A 32bp-barcoded sindbis virus is injected in the primary somatosensory cortex of P14, P9 and P7 pups. The virus enter the neurons, replicate and migrate to the terminal connections. Then, S1 cells are FACS-sorted and their transcriptome is sequenced using Fluidigm integrated fluidic circuits on C1 system. In addition, 6 projection targets where S1 cells are expected to project are dissected and barcodes of the Sindbis viruses are sequenced by bulk RNA-seq. This allow to link the transcriptome of S1-cells to their projection targets.