<scp>RNA</scp> polymerase <scp>V</scp> targets transcriptional silencing components to promoters of protein‐coding genes

Zheng, Qi; Rowley, M. Jordan; Böhmdorfer, Gudrun; Sandhu, D. P. S.; Gregory, Brian D.; Wierzbicki, Andrzej

doi:10.1111/tpj.12034

Cited by 67 publications

(93 citation statements)

References 45 publications

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“…This suggests that RdDM may not be a crucial requirement for silencing all transposons (5,6,30). Instead, this activity may be critical for maintaining the silencing of the transposons that are located near genes (31). Indeed, the analysis of changes in DNA methylation in the mop1 and mop3 mutants that perturb components of the maize RdDM system revealed that the loss of mCHH at the transposon edges near genes can often result in additional loss of CG/CHG methylation in the transposon.…”

Section: Resultsmentioning

confidence: 99%

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Gent

Zynda

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

191

249

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The maize genome is relatively large (∼2.3 Gb) and has a complex organization of interspersed genes and transposable elements, which necessitates frequent boundaries between different types of chromatin. The examination of maize genes and conserved noncoding sequences revealed that many of these are flanked by regions of elevated asymmetric CHH (where H is A, C, or T) methylation (termed mCHH islands). These mCHH islands are quite short (∼100 bp), are enriched near active genes, and often occur at the edge of the transposon that is located nearest to genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications revealed that mCHH islands mark the transition from heterochromatin-associated modifications to euchromatin-associated modifications. The presence of an mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of insertion/ deletions in promoters often influences the presence and position of an mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities and are lost in mop1 and mop3 mutants, but the nearby genes rarely exhibit altered expression levels. Instead, loss of an mCHH island is often accompanied by additional loss of DNA methylation in CG and CHG contexts associated with heterochromatin in nearby transposons. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of nearby genes.T he cytosine bases in a genome can be modified to 5-methylcytosine by adding a methyl group at the 5′ position. This process, called DNA methylation, is conserved from algae to animals and plants (1, 2). DNA methylation can be separated into different types based on the local sequence context. In plants DNA methylation is found at the symmetric CG or CHG (where H = A, C, or T) sites or at nonsymmetric CHH sites. CG and CHG methylation are maintained at high fidelity following DNA replication due to activity of maintenance methyltransferases such as MET1 or chromomethylase (CMT) 3 (3, 4), whereas CHH methylation (mCHH) requires targeting by either domains rearranged methylase 2 (DRM2) or CMT2 (3-6). The DRM2 targeting occurs via RNAdirected DNA methylation (RdDM) and requires the activity of polymerase IV (PolIV) and polymerase V (PolV) complexes (3, 4). There is evidence that recruitment of PolIV and PolV may require the presence of dimethylation of lysine 9 of histone H3 (H3K9me2) or DNA methylation at the targeted genomic regions (7,8). The specific mechanisms that recruit CMT2 are not well characterized but may require specific histone modifications (5, 6).Much of our knowledge of DNA methylation in plants is derived from studies of the model plant Arabidopsis thaliana, which has a relatively small genome and relatively few examples of genes with nearby transposons (36.3%; ref. 9). The maize genome is much more complex, with the majority (85.5%) of genes positioned within 1...

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Section: Resultsmentioning

confidence: 99%

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Gent

Zynda

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

191

249

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“…Recent studies from Arabidopsis further suggest that RdDM is enriched in specific genomic contexts such as recently inserted transposons and promoters (Zheng et al, 2012;Zhong et al, 2012). In maize, both 24-nucleotide siRNAs and CHH methylation are more abundant near genes than in the expanses of repetitive intergenic DNA, giving rise to the term CHH islands (Gent et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…RdDM is primarily associated with the repression of transposons, but it can indirectly affect gene expression through genomic imprinting (Vu et al, 2013) and paramutation (reviewed in Hollick, 2012). Multiple studies have suggested that RdDM is not a uniform feature of heterochromatin in plant genomes but is enriched in particular heterochromatic regions, including 5S ribosomal loci, long terminal repeats of retrotransposons, DNA transposons, and repetitive elements in general when close to genes (Onodera et al, 2005;Zheng et al, 2012;Zhong et al, 2012;Gent et al, 2013;Regulski et al, 2013;Stroud et al, 2013;Sun et al, 2013;Zemach et al, 2013;Diez et al, 2014;Wei et al, 2014). In Arabidopsis, methylation in long transposons near centromeres can be mediated by the DNA methyltransferase CMT2 without the involvement of RdDM (Zemach et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

et al. 2014

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RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.

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“…The use of null mutants to control for nonspecific antibody binding in ChiP-seq studies in Arabidopsis seedlings demonstrated that many peaks are false-positives (Wierzbicki et al, 2012;Zheng et al, 2012). Efficient siRNA would be required for this approach to be adopted in mammalian cell culture.…”

Section: General Features Of Genome-wide Tcf Bindingmentioning

confidence: 99%

Finding a Needle in a Genomic Haystack

Bhambhani¹,

Cadigan²

2014

WNT Signaling in Development and Disease

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RNA polymerase V targets transcriptional silencing components to promoters of protein‐coding genes

Cited by 67 publications

References 45 publications

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

Finding a Needle in a Genomic Haystack

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