Differential epigenetic regulation within an Arabidopsis retroposon family

We previously reported a novel family of Arabidopsis thaliana nonautonomous retroposons, Sadhu, showing epigenetic variation in natural populations. Here, we show that transcripts corresponding to Sadhu elements accumulate in a subset of mutants carrying disruptions in genes encoding chromatin modif...

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Published in:Genetics (Austin) Vol. 176; no. 1; pp. 151 - 160
Main Authors: Rangwala, S.H, Richards, E.J
Format: Journal Article
Language:English
Published: United States Genetics Soc America 01.05.2007
Genetics Society of America
Copyright © 2007 by the Genetics Society of America
Subjects:
Arabidopsis
Arabidopsis - genetics
Arabidopsis thaliana
Base Pairing
Base Pairing - genetics
Chromatin
Chromatin - genetics
Chromatin Immunoprecipitation
Chromosome Mapping
cytosine
Cytosine - metabolism
Deoxyribonucleic acid
DNA
DNA Methylation
Epigenesis, Genetic
epigenetics
gene expression
Gene Expression Regulation, Plant
gene silencing
Genetics
Genome, Plant
Genome, Plant - genetics
Genomics
Histones
Histones - metabolism
Investigations
Lysine
Lysine - metabolism
messenger RNA
metabolism
Methylation
Molecular Sequence Data
Mutants
Mutation
Mutation - genetics
Natural populations
nucleotide sequences
Retroelements
Retroelements - genetics
retrotransposons
ISSN:0016-6731, 1943-2631, 1943-2631
Online Access:Get full text
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Summary:We previously reported a novel family of Arabidopsis thaliana nonautonomous retroposons, Sadhu, showing epigenetic variation in natural populations. Here, we show that transcripts corresponding to Sadhu elements accumulate in a subset of mutants carrying disruptions in genes encoding chromatin modification enzymes, but are not significantly expressed in mutants defective in RNA silencing pathways, indicating that RNA-directed processes are not necessary to maintain transcriptional suppression of this class of retroelements. We focused our analysis on three representative elements showing differential responses to ddm1, met1, and hda6 mutations. These mutations had differing effects on cytosine methylation depending on the element and the sequence context. Curiously, the Sadhu6-1 element with the strongest CpHpG methylation is expressed in a met1 CpG methyltransferase mutant, but is not expressed in ddm1 or cmt3 mutants. Regardless of the mutant background, H3meK9 was found at silenced loci, while H3meK4 was restricted to expressed alleles. We discuss the different modes of regulation within this family and the potential impact of this regulation on the stability of silencing in natural populations.
Bibliography:http://www.genetics.org/
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Corresponding author: Department of Biology, Campus Box 1137, Washington University, 1 Brookings Dr., St. Louis, MO 63130. E-mail: richards@wustl.edu
Communicating editor: T. P. Brutnell
Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. DY230445, DY230446, EC268296, EC613982, EC613983, EC613984TH, EC613985, and EC613986.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.107.071092