Epigenomic tomography for probing spatially defined chromatin state in the brain
| dc.contributor.author | Liu, Zhengzhi | en |
| dc.contributor.author | Deng, Chengyu | en |
| dc.contributor.author | Zhou, Zirui | en |
| dc.contributor.author | Ya, Xiao | en |
| dc.contributor.author | Jiang, Shan | en |
| dc.contributor.author | Zhu, Bohan | en |
| dc.contributor.author | Naler, Lynette B. | en |
| dc.contributor.author | Jia, Xiaoting | en |
| dc.contributor.author | Yao, Danfeng (Daphne) | en |
| dc.contributor.author | Lu, Chang | en |
| dc.date.accessioned | 2024-09-16T17:21:29Z | en |
| dc.date.available | 2024-09-16T17:21:29Z | en |
| dc.date.issued | 2024-03-25 | en |
| dc.description.abstract | Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Singlecell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome. | en |
| dc.description.sponsorship | The study was partly supported by US National Institutes of Health grants R01GM141096 (C.L.), R01DA056187 (C.L.), and R01NS123069 (X.J.). The authors also acknowledge support from College of Engineering and Institute for Critical Technology and Applied Science at Virginia Tech. | en |
| dc.description.version | Published version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier.doi | https://doi.org/10.1016/j.crmeth.2024.100738 | en |
| dc.identifier.uri | https://hdl.handle.net/10919/121137 | en |
| dc.identifier.volume | 4 | en |
| dc.language.iso | en | en |
| dc.publisher | Cell Press | en |
| dc.rights | Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International | en |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | en |
| dc.title | Epigenomic tomography for probing spatially defined chromatin state in the brain | en |
| dc.title.serial | Cell Reports Methods | en |
| dc.type | Article - Refereed | en |
| dc.type.dcmitype | Text | en |