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H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana

Jennifer M. Frost, Jaehoon Lee, Ping-Hung Hsieh, Samuel J. H. Lin, Yunsook Min, Matthew Bauer, Anne M. Runkel, Hyung-Taeg Cho, View ORCID ProfileTzung-Fu Hsieh, Yeonhee Choi, Robert L. Fischer
doi: https://doi.org/10.1101/2023.01.08.523178
Jennifer M. Frost
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
6Genomics and Child Health, Queen Mary University of London, London, United Kingdom
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  • For correspondence: j.frost@qmul.ac.uk yhc@snu.ac.kr rfischer@berkeley.edu
Jaehoon Lee
2Department of Biological Sciences, Seoul National University, Seoul, Korea
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Ping-Hung Hsieh
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
7DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
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Samuel J. H. Lin
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
8Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States
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Yunsook Min
2Department of Biological Sciences, Seoul National University, Seoul, Korea
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Matthew Bauer
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
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Anne M. Runkel
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
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Hyung-Taeg Cho
2Department of Biological Sciences, Seoul National University, Seoul, Korea
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Tzung-Fu Hsieh
3Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
4Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, United States
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Yeonhee Choi
2Department of Biological Sciences, Seoul National University, Seoul, Korea
5Research Center for Plant Plasticity, Seoul National University, Seoul, Korea
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  • For correspondence: j.frost@qmul.ac.uk yhc@snu.ac.kr rfischer@berkeley.edu
Robert L. Fischer
1Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
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  • For correspondence: j.frost@qmul.ac.uk yhc@snu.ac.kr rfischer@berkeley.edu
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Abstract

H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction, though it is not known how FACT targets DME sites. Here, we investigated whether H2AX is involved in DME- and FACT-mediated DNA demethylation during Arabidopsis reproduction. We show that h2a.x mutants are more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to the Green Fluorescent Protein (GFP) gene under the H2A.X promoter was highly expressed in newly developing Arabidopsis tissues, including in male and female gametophytes. We examined DNA methylation in h2a.x developing seeds using whole genome bisulfite sequencing, and found that CG DNA methylation in the developing endosperm, but not the embryo, is decreased genome-wide in h2a.x mutants, predominately in transposons and intergenic DNA. Hypomethylated sites overlapped 62 % with canonical DME loci. These data indicate that H2A.X is not required for DME function, but is important for DNA methylation homeostasis in the unique chromatin environment of Arabidopsis endosperm.

Competing Interest Statement

The authors have declared no competing interest.

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Posted January 09, 2023.
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H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana
Jennifer M. Frost, Jaehoon Lee, Ping-Hung Hsieh, Samuel J. H. Lin, Yunsook Min, Matthew Bauer, Anne M. Runkel, Hyung-Taeg Cho, Tzung-Fu Hsieh, Yeonhee Choi, Robert L. Fischer
bioRxiv 2023.01.08.523178; doi: https://doi.org/10.1101/2023.01.08.523178
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H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana
Jennifer M. Frost, Jaehoon Lee, Ping-Hung Hsieh, Samuel J. H. Lin, Yunsook Min, Matthew Bauer, Anne M. Runkel, Hyung-Taeg Cho, Tzung-Fu Hsieh, Yeonhee Choi, Robert L. Fischer
bioRxiv 2023.01.08.523178; doi: https://doi.org/10.1101/2023.01.08.523178

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