Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1)

Singer, Tatjana; Yordan, C.; Martienssen, Robert A.

doi:10.1101/gad.193701

Cited by 294 publications

(248 citation statements)

References 57 publications

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“…None of the MULEs that are the closest Jit relatives encode a B function, yet these elements can move, at least in Arabidopsis ddm1 mutants (Singer et al, 2001). Lisch (2002) has summarized other evidence that suggests that these elements are or recently have been active in various angiosperm species, including the identification of apparently complete MULEs in rice, barley (Hordeum vulgare), sorghum (Sorghum bicolor), and lotus (Lotus corniculatus); the occurrence of ESTs corresponding to MULEs in EST databases, and the identification of nearly identical copies of several elements in species with almost completely sequenced genomes.…”

Section: Mutator Linesmentioning

confidence: 99%

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

Yan

Maurais

et al. 2004

Plant Cell

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The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit). Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.

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Section: Mutator Linesmentioning

confidence: 99%

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

Yan

Maurais

et al. 2004

Plant Cell

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“…Historically, DNA methylation has been proposed to be a defense mechanism adopted by genomes against selfish DNA elements (Goll and Bestor 2005). Indeed, transposons and other retroelements are generally methylated and loss of methylation at these elements leads to increased transposition (Miura et al 2001;Singer et al 2001;Kato et al 2003;Zhang et al 2006). In addition to its role in protecting genome integrity, DNA methylation has also been implicated in the regulation of gene expression (Bird 2002;Zhang et al 2006;Zilberman et al 2007).…”

mentioning

confidence: 99%

Progressive Loss of DNA Methylation Releases Epigenetic Gene Silencing From a Tandemly Repeated Maize Myb Gene

Sekhon¹,

Chopra

2009

Genetics

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Maize pericarp color1 (p1) gene, which regulates phlobaphene biosynthesis in kernel pericarp and cob glumes, offers an excellent genetic system to study tissue-specific gene regulation. A multicopy p1 allele, P1-wr (white pericarp/red cob) is epigenetically regulated. Hypomethylation of P1-wr in the presence of Unstable factor for orange1 (Ufo1), leads to ectopic pigmentation of pericarp and other organs. The Ufo1-induced phenotypes show incomplete penetrance and poor expressivity: gain of pigmentation is observed only in a subset of plants carrying Ufo1 mutation, and the extent of pigmentation is highly variable. We show that Ufo1 induces progressive hypomethylation of P1-wr repeats over generations. After five generations of exposure to Ufo1, a 30-40% decrease in CG and CNG methylation was observed in an upstream enhancer and an intron region of P1-wr. Interestingly, such hypomethylation correlated with an increase in penetrance of the Ufo1-induced pigmentation phenotype from $27 to 61%. Expressivity of the Ufo1-induced phenotype also improved markedly as indicated by increased uniformity of pericarp pigmentation in the later generations. Furthermore, the poor expressivity of the Uo1 is associated with mosaic methylation patterns of the P1-wr upstream enhancer in individual cells and distinct P1-wr gene copies. Finally, comparison of methylation among different tissues indicated that Ufo1 induces rapid CG and CNG hypomethylation of P1-wr repeats during plant development. Together, these data indicate that the poor penetrance and expressivity of Ufo1-induced phenotypes is caused by mosaicism of methylation, and progressive mitotic hypomethylation leads to improved meiotic heritability of the mutant phenotype. In duplicated genomes like maize, loss of an epigenetic regulator may produce mosaic patterns due to redundancy of epigenetic regulators and their target sequences. We show here that multiple developmental cycles may be required for complete disruption of suppressed epigenetic states and appearance of heritable phenotypes.

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“…One level of control is exerted by posttranscriptional turnover of element transcripts through RNA interference (RNAi) (Sijen and Plasterk 2003;Almeida and Allshire 2005). Transposons are also controlled epigenetically by altering the accessibility of the elements to the transcriptional machinery and transposases through cytosine hypermethylation and differential chromatin modification and packaging (Hirochika et al 2000;Miura et al 2001;Singer et al 2001;Lippman et al 2003;Kato et al 2004). Subsequent accumulation of mutations within epigenetically silenced elements leads to their irreversible inactivation.…”

mentioning

confidence: 99%

“…Therefore, it is likely that CMT3 provides a link between chromatin level and DNA methylation silencing. Other chromatin modifying enzymes that act in transposon silencing include Decrease in DNA Methylation 1 (DDM1) (Miura et al 2001;Singer et al 2001;Gendrel et al 2002;Lippman et al 2003), a SWI2/SNF2 chromatin remodeling protein, and HDA6, an RPD3-class histone deacetylase (Lippman et al 2003). Furthermore, because DRM2-directed de novo methylation is thought to be directed by the RNA silencing pathway ), Tranet al (2005 proposed that an RNA-directed pathway might silence dispersed transposable elements in otherwise unsilenced regions of the genome.…”

mentioning

confidence: 99%

Differential Epigenetic Regulation Within an Arabidopsis Retroposon Family

Rangwala

Richards

2007

Genetics

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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.

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Robertson's Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1)

Cited by 294 publications

References 57 publications

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion

Progressive Loss of DNA Methylation Releases Epigenetic Gene Silencing From a Tandemly Repeated Maize Myb Gene

Differential Epigenetic Regulation Within an Arabidopsis Retroposon Family

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