SCOPE-C reveals long-range enhancer networks emerging as key regulators during human cortical neurogenesis

Abstract

Chromatin in the human brain cortex shows more enhancer-enhancer contacts than in macaques and mice, yet the organization of these contacts across cellular states and the mechanisms behind them remain unclear. Here, we developed simultaneous conformation and open-chromatin capture (SCOPE-C) to map open chromatin and its long-range spatial interactions from low-input samples. Applying SCOPE-C to fetal cortical cells from humans, macaques, and mice, we reveal that human neurogenesis is characterized by extended long-range (>1 megabase [Mb]) enhancer-promoter loops formed via CCCTC-binding factor (CTCF) mediated loop extrusion. In human excitatory neurons (ENs), these interactions establish dynamic networks spanning up to 10 Mb. These networks are enriched with human-biased enhancers and neuropsychiatric disorder-linked single-nucleotide polymorphisms (SNPs) regulating key cell-fate genes such as SATB2. The formation of these vast, dynamic enhancer networks appears to be a prominent feature of human ENs, offering mechanistic insights into cortical evolution and the genetic vulnerability of neurodevelopmental regulation.

Keywords: 3D genome; cortical neurogenesis; enhancer network; human brain evolution.