Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN
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497_2018_Article_358.pdf
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2.03 MB
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Adobe PDF
Checksum (MD5)
c176950917890fc42a55c1cf95dfd7da
Author(s)
Zheng, Xiao-yu
Gehring, Mary
Date Issued
February 2019
Journal
Plant Reproduction
Publisher
Springer Berlin Heidelberg
Citation
Zheng, Xiao-yu and Mary Gehring. “Low-Input Chromatin Profiling in Arabidopsis Endosperm Using CUT&RUN.” Plant Reproduction (February 2019): 1-13 © 2019 The Author(s)
Version
Final published version
Abstract
Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. In Arabidopsis, profiling the epigenetic landscape of endosperm on a genome-wide scale is challenging due to its small size, mode of development and close association with maternal tissue. Here, we applied a low-input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using limited numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN make it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable further study of tissue- or cell-type-specific epigenomes in Arabidopsis and other plant species.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1007/s00497-018-00358-1
