Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN

• DOI: 10.1007/s00497-018-00358-1
• Publication Date: 2019-02-05T03:07:04Z
• Authors: Xiao-yu Zheng; Mary Gehring
• Keywords: Epigenomics; Chromatin immunoprecipitation; Genomic Imprinting

Application of a low-input chromatin profiling method, CUT&RUN, to FACS-purified Arabidopsis endosperm nuclei generates parental-specific genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility. Endosperm is an essential seed tissue unique epigenetic landscape. During development, differential regulation the maternal paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. In Arabidopsis, landscape on scale challenging due its small size, mode development close association tissue. Here, we applied CUT&RUN (cleavage under targets release using nuclease), profile modifications limited numbers nuclei. We demonstrate that reproducibility around 20,000 purified by flow cytometry fluorescence-activated cell sorting. peaks identified previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, some distinctions heterochromatin. The versatility simplicity make it viable alternative ChIP, which requires greater amounts starting material, will enable further study tissue- or cell-type-specific epigenomes other plant species.