- Song, Michael;
- Pebworth, Mark-Phillip;
- Yang, Xiaoyu;
- Abnousi, Armen;
- Fan, Changxu;
- Wen, Jia;
- Rosen, Jonathan D;
- Choudhary, Mayank NK;
- Cui, Xiekui;
- Jones, Ian R;
- Bergenholtz, Seth;
- Eze, Ugomma C;
- Juric, Ivan;
- Li, Bingkun;
- Maliskova, Lenka;
- Lee, Jerry;
- Liu, Weifang;
- Pollen, Alex A;
- Li, Yun;
- Wang, Ting;
- Hu, Ming;
- Kriegstein, Arnold R;
- Shen, Yin
Lineage-specific epigenomic changes during human corticogenesis have been difficult to study owing to challenges with sample availability and tissue heterogeneity. For example, previous studies using single-cell RNA sequencing identified at least 9 major cell types and up to 26 distinct subtypes in the dorsal cortex alone1,2. Here we characterize cell-type-specific cis-regulatory chromatin interactions, open chromatin peaks, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational samples of the human cortex. We show that chromatin interactions underlie several aspects of gene regulation, with transposable elements and disease-associated variants enriched at distal interacting regions in a cell-type-specific manner. In addition, promoters with increased levels of chromatin interactivity-termed super-interactive promoters-are enriched for lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of transcription. Finally, we develop CRISPRview, a technique that integrates immunostaining, CRISPR interference, RNAscope, and image analysis to validate cell-type-specific cis-regulatory elements in heterogeneous populations of primary cells. Our findings provide insights into cell-type-specific gene expression patterns in the developing human cortex and advance our understanding of gene regulation and lineage specification during this crucial developmental window.