Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways

Sarah N Anderson, Gregory J. Zynda, Jawon Song, Zhaoxue Han, Matthew W. Vaughn, Qing Li, Nathan M Springer

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

Original languageEnglish (US)
Pages (from-to)1921-1932
Number of pages12
JournalG3: Genes, Genomes, Genetics
Volume8
Issue number6
DOIs
StatePublished - Jun 1 2018

Fingerprint

DNA Methylation
Zea mays
RNA
Genes
Methylation
chromomethylase
Endosperm
Gene Expression Regulation
Gene Expression Profiling
Transcriptome
Islands
Epigenomics
Chromatin
Reproduction
Alleles
Genotype

Keywords

  • DNA methylation chromomethylase
  • Methylation maize
  • RNA directed DNA
  • Transposable elements

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

Cite this

Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways. / Anderson, Sarah N; Zynda, Gregory J.; Song, Jawon; Han, Zhaoxue; Vaughn, Matthew W.; Li, Qing; Springer, Nathan M.

In: G3: Genes, Genomes, Genetics, Vol. 8, No. 6, 01.06.2018, p. 1921-1932.

Research output: Contribution to journalArticle

Anderson, Sarah N ; Zynda, Gregory J. ; Song, Jawon ; Han, Zhaoxue ; Vaughn, Matthew W. ; Li, Qing ; Springer, Nathan M. / Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways. In: G3: Genes, Genomes, Genetics. 2018 ; Vol. 8, No. 6. pp. 1921-1932.
@article{4d0f0ac4a90f4ea99250b36c7f7aafe7,
title = "Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways",
abstract = "DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.",
keywords = "DNA methylation chromomethylase, Methylation maize, RNA directed DNA, Transposable elements",
author = "Anderson, {Sarah N} and Zynda, {Gregory J.} and Jawon Song and Zhaoxue Han and Vaughn, {Matthew W.} and Qing Li and Springer, {Nathan M}",
year = "2018",
month = "6",
day = "1",
doi = "10.1534/g3.118.200284",
language = "English (US)",
volume = "8",
pages = "1921--1932",
journal = "G3: Genes, Genomes, Genetics",
issn = "2160-1836",
publisher = "Genetics Society of America",
number = "6",

}

TY - JOUR

T1 - Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways

AU - Anderson, Sarah N

AU - Zynda, Gregory J.

AU - Song, Jawon

AU - Han, Zhaoxue

AU - Vaughn, Matthew W.

AU - Li, Qing

AU - Springer, Nathan M

PY - 2018/6/1

Y1 - 2018/6/1

N2 - DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

AB - DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.

KW - DNA methylation chromomethylase

KW - Methylation maize

KW - RNA directed DNA

KW - Transposable elements

UR - http://www.scopus.com/inward/record.url?scp=85047846779&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85047846779&partnerID=8YFLogxK

U2 - 10.1534/g3.118.200284

DO - 10.1534/g3.118.200284

M3 - Article

C2 - 29618467

AN - SCOPUS:85047846779

VL - 8

SP - 1921

EP - 1932

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

SN - 2160-1836

IS - 6

ER -