Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers
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Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers. / Xie, Yeming; Ruan, Fengying; Li, Yaning; Luo, Meng; Zhang, Chen; Chen, Zhichao; Xie, Zhe; Weng, Zhe; Chen, Weitian; Chen, Wenfang; Fang, Yitong; Sun, Yuxin; Guo, Mei; Wang, Juan; Xu, Shouping; Wang, Hongqi; Tang, Chong.
In: eLife, Vol. 12, RP87868, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers
AU - Xie, Yeming
AU - Ruan, Fengying
AU - Li, Yaning
AU - Luo, Meng
AU - Zhang, Chen
AU - Chen, Zhichao
AU - Xie, Zhe
AU - Weng, Zhe
AU - Chen, Weitian
AU - Chen, Wenfang
AU - Fang, Yitong
AU - Sun, Yuxin
AU - Guo, Mei
AU - Wang, Juan
AU - Xu, Shouping
AU - Wang, Hongqi
AU - Tang, Chong
N1 - Publisher Copyright: © 2023, Xie, Ruan, Li et al.
PY - 2024
Y1 - 2024
N2 - As the genome is organized into a three-dimensional structure in intracellular space, epigenomic information also has a complex spatial arrangement. However, most epigenetic studies describe locations of methylation marks, chromatin accessibility regions, and histone modifications in the horizontal dimension. Proper spatial epigenomic information has rarely been obtained. In this study, we designed spatial chromatin accessibility sequencing (SCA-seq) to resolve the genome conformation by capturing the epigenetic information in single-molecular resolution while simultaneously resolving the genome conformation. Using SCA-seq, we are able to examine the spatial interaction of chromatin accessibility (e.g. enhancer-promoter contacts), CpG island methylation, and spatial insulating functions of the CCCTC-binding factor. We demonstrate that SCA-seq paves the way to explore the mechanism of epigenetic interactions and extends our knowledge in 3D packaging of DNA in the nucleus.
AB - As the genome is organized into a three-dimensional structure in intracellular space, epigenomic information also has a complex spatial arrangement. However, most epigenetic studies describe locations of methylation marks, chromatin accessibility regions, and histone modifications in the horizontal dimension. Proper spatial epigenomic information has rarely been obtained. In this study, we designed spatial chromatin accessibility sequencing (SCA-seq) to resolve the genome conformation by capturing the epigenetic information in single-molecular resolution while simultaneously resolving the genome conformation. Using SCA-seq, we are able to examine the spatial interaction of chromatin accessibility (e.g. enhancer-promoter contacts), CpG island methylation, and spatial insulating functions of the CCCTC-binding factor. We demonstrate that SCA-seq paves the way to explore the mechanism of epigenetic interactions and extends our knowledge in 3D packaging of DNA in the nucleus.
KW - 3D genome
KW - chromatin accessibility
KW - chromosomes
KW - DNA methylation
KW - gene expression
KW - GpC methyltransferase
KW - Hi-C
KW - human
KW - pore-C
U2 - 10.7554/eLife.87868
DO - 10.7554/eLife.87868
M3 - Journal article
C2 - 38236718
AN - SCOPUS:85177826809
VL - 12
JO - eLife
JF - eLife
SN - 2050-084X
M1 - RP87868
ER -
ID: 381060805