Spatial epigenome–transcriptome co-profiling of mammalian tissues

Zhang, Di; Deng, Yanxiang; Kukanja, Petra; Agirre, Eneritz; Bartošovič, Marek; Dong, Mingze; Ma, Cong; Ma, Sai; Su, Graham; Bao, Shuozhen; Liu, Yang; Xiao, Yang; Rosoklija, Gorazd; Dwork, Andrew J.; Mann, J. John; Leong, Kam W.; Boldrini, Maura; Wang, Liya; Haeussler, Maximilian; Raphael, Benjamin J.; Kluger, Yuval; Castelo‐Branco, Gonçalo; Fan, Rong

doi:10.1038/s41586-023-05795-1

articleNatureMar 15, 2023HYBRID OA

Spatial epigenome–transcriptome co-profiling of mammalian tissues

DZDi Zhang YDYanxiang Deng PKPetra Kukanja EAEneritz Agirre MBMarek Bartošovič

Yale University · Yale Cancer Center · +12 more institutions

PubMed

Indexed incrossrefpubmed

Abstract

. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly…

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Topics & keywords

Topics

Keywords

Epigenome
Epigenomics
Transcriptome
Biology
Epigenetics
Chromatin
Computational biology
H3K4me3

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