Joint epigenome profiling reveals cell-type-specific gene regulatory programs in human cortical organoids

Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomic methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a novel approach, 3DRAM-seq, which simultaneously interrogates spatial genome organization, chromatin accessibility, DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA-seq in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay (MPRA) to profile cell-type-specific enhancer activity in organoids and functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues. Simultaneous measurement of gene expression, DNA accessibility, DNA methylation and 3D genome architecture using 3DRAM-seq in mouse embryonic stem cells (mESC) and sorted cell populations, namely radial glia cells (RGC) and intermediate progenitor cells (IPC), from human cortical organoids. Additionally, massive parallel reporter assay in NSC, IPC and PAX6/SOX2/EOMES triple negative cell population isolated from electroporated human cortical organoids.