A medial entorhinal connectome reveals compartmentalized microcircuit architecture

Abstract

The medial entorhinal cortex (MEC) transforms multimodal inputs into spatial representations, but the synaptic architecture underlying its computations remains unclear. Here we generated a synapse-resolution connectomic dataset spanning all six layers of mouse MEC and the adjacent parasubiculum with serial electron microscopy, providing a continuous volume for mapping cellular organization and connectivity across layers and regions. We found that clustered pyramidal neurons in MEC layer II extended oblique apical dendrites with a dorsolateral bias and long-range myelinated axons within the layer. Exhaustive reconstruction of one cluster revealed a central exclusion core (ExC) that spatially partitioned basal dendritic architecture and synaptic connectivity. A spatially constrained growth model reproduced the position-dependent dendritic patterns. Within the ExC, pyramidal neurons formed a compact recurrent excitatory network and converged onto shared inhibitory partners. Basket cells (BC) and recurrent Martinotti cells provided perisomatic and apical-dendritic feedback, respectively. Dense, compact reciprocal connectivity between L2P neurons and BCs within the ExC, together with BC axonal bands extending beyond the ExC, suggests a potential circuit mechanism for generating temporally structured inhibitory output from the pyramidal-cell cluster along directionally extended axons. Together, these findings link cellular-scale geometry and synaptic wiring to emergent circuit dynamics that extend from dense computation within individual clusters to region-wide modulation, providing a connectomic foundation for understanding the circuit basis of spatial navigation.