BGI Genomics, BGI-Shenzhen, Shenzhen, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
Zhe Xie
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Department of Biology, Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
Zhe Weng
BGI Genomics, BGI-Shenzhen, Shenzhen, China
Weitian Chen
BGI Genomics, BGI-Shenzhen, Shenzhen, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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.
