Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants

Andrew Read, Trevor J Weiss, Peter Crisp, Zhikai Liang, Jaclyn Noshay, Claire C. Menard, Chunfang Wang, Meredith Song, Candice N Hirsch, Nathan M. Springer, Feng Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole-genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for the locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild-type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.

Original languageEnglish (US)
Pages (from-to)103-116
Number of pages14
JournalPlant Journal
Volume111
Issue number1
DOIs
StatePublished - Jul 2022

Bibliographical note

Funding Information:
Peter Hermanson contributed to the molecular analyses that were important for this study. Michelle Stitzer provided helpful comments and discussion regarding the DST1 TE family. The Minnesota Supercomputing Institute at the University of Minnesota provided computational resources that contributed to this research. MS was supported by the Undergraduate Research Opportunities Program (UROP) from the University of Minnesota. This work was funded by NSF IOS-1934384 to NMS and CNH. AR is supported by NSF PRFB IOS-2109697.

Funding Information:
Peter Hermanson contributed to the molecular analyses that were important for this study. Michelle Stitzer provided helpful comments and discussion regarding the DST1 TE family. The Minnesota Supercomputing Institute at the University of Minnesota provided computational resources that contributed to this research. MS was supported by the Undergraduate Research Opportunities Program (UROP) from the University of Minnesota. This work was funded by NSF IOS‐1934384 to NMS and CNH. AR is supported by NSF PRFB IOS‐2109697.

Publisher Copyright:
© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Keywords

  • DNA methylation
  • Setaria viridis
  • epigenetics
  • genome editing
  • transposable element

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