1. Temporally distinct 3D multi-omic dynamics in the developing human brain.
- Author
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Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, and Luo C
- Subjects
- Humans, Cell Differentiation genetics, Disease Susceptibility, Epigenomics, Fetus cytology, Fetus embryology, Fetus metabolism, Neuroglia metabolism, Neuroglia cytology, Neurons metabolism, Neurons cytology, Schizophrenia genetics, Schizophrenia metabolism, Single Molecule Imaging, Single-Cell Analysis, Time Factors, Infant, Newborn, Chromatin metabolism, Chromatin genetics, Chromatin chemistry, DNA Methylation genetics, Epigenesis, Genetic, Hippocampus cytology, Hippocampus embryology, Hippocampus growth & development, Hippocampus metabolism, Multiomics, Prefrontal Cortex cytology, Prefrontal Cortex embryology, Prefrontal Cortex growth & development, Prefrontal Cortex metabolism
- Abstract
The human hippocampus and prefrontal cortex play critical roles in learning and cognition
1,2 , yet the dynamic molecular characteristics of their development remain enigmatic. Here we investigated the epigenomic and three-dimensional chromatin conformational reorganization during the development of the hippocampus and prefrontal cortex, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation generated by single-nucleus methyl-3C sequencing (snm3C-seq3)3 . The remodelling of DNA methylation is temporally separated from chromatin conformation dynamics. Using single-cell profiling and multimodal single-molecule imaging approaches, we have found that short-range chromatin interactions are enriched in neurons, whereas long-range interactions are enriched in glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type development and differentiation, finding putatively causal common variants for schizophrenia strongly overlapping with chromatin loop-connected, cell-type-specific regulatory regions. Our data provide multimodal resources for studying gene regulatory dynamics in brain development and demonstrate that single-cell three-dimensional multi-omics is a powerful approach for dissecting neuropsychiatric risk loci., Competing Interests: Competing interests J.R.E. serves on the scientific advisory board of Zymo Research. A.D.S. is an employee of Arima Genomics., (© 2024. The Author(s).)- Published
- 2024
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