Tissue- and Expression Level–Specific Chromatin Looping at Maize<i>b1</i>Epialleles

Louwers, Marieke; Bader, Rechien; Haring, Max; Driel, Roel van; Laat, Wouter de; Stam, Maike

doi:10.1105/tpc.108.064329

Cited by 128 publications

(144 citation statements)

References 45 publications

Supporting

Mentioning

137

Contrasting

Order By: Relevance

“…Moreover, whereas B-I reverts spontaneously to B 0 at high frequency (1-10%) and can thus be considered a metastable epiallele, B 0 is highly stable and only becomes more active in RNAi mutant backgrounds (Dorweiler et al, 2000;Alleman et al, 2006;Woodhouse et al, 2006). These findings suggest that the tandem repeats of B-I and B 0 are, respectively, just below and well above the threshold required for RNAi-dependent chromatin targeting, presumably as a consequence of differences in chromatin states (Stam et al, 2002;Louwers et al, 2009). Although the available evidence seems to indicate otherwise (Arteaga-Vazquez and Chandler, 2010), it is also reasonable to assume that the tandem repeats of B 0 and B-I produce distinct amount of siRNAs, at least during the reproductive phase, when the RNAi-dependent chromatin targeting pathway could be most active, as in Arabidopsis (Figure 2).…”

Section: Variation In Rddm Strength and Paramutationmentioning

confidence: 79%

“…This allele exists in two epiallelic forms, B-I and B 0 , which are strongly and weakly active, respectively. Difference in expression is associated with differential DNA methylation and chromatin accessibility of a set of seven tandem repeats that act as enhancers and that are located 100 kb upstream of the b1 transcription start site (Stam et al, 2002;Louwers et al, 2009). These seven tandem repeats are responsible for mediating in F1 heterozygotes the transfer of the expression state of paramutagenic B 0 to paramutable B-I with 100% penetrance and in an RNAi-dependent manner.…”

Section: Variation In Rddm Strength and Paramutationmentioning

confidence: 99%

See 1 more Smart Citation

Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

View full text Add to dashboard Cite

DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway. Heredity (2010) 105, 14-23; doi:10.1038/hdy.2010.52; published online 12 May 2010Keywords: DNA methylation; repeat elements; Arabidopsis; RNAi; paramutation Introduction DNA methylation refers to the enzymatic transfer of a methyl group to specific nucleotides within the DNA sequence. In eukaryotes, this modification almost exclusively affects cytosines. Although clearly ancestral, cytosine methylation is not universally present in the eukaryotic tree of life. Thus, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as the nematode Caenorhabditis elegans have no DNA methyltransferases (DNA MTases;Goll and Bestor, 2005). Furthermore, Drosophila contains a single, enigmatic DNA MTase-like protein (Goll and Bestor, 2005) and it is unclear if this species actually methylates DNA. By contrast, DNA methylation is readily detected in plants and mammals, where it is critical for normal development and genome stability. Although numerous hypotheses have been proposed (Bird, 1995;Yoder et al., 1997;Martienssen, 1998;Regev et al., 1998;Colot and Rossignol, 1999;Suzuki and Bird, 2008), it is still a mystery as to why these organisms cannot dispense with cytosine methylation when many lower eukaryotes can.In plants and mammals, most methylated cytosines are found over repeat elements (Goll and Bestor, 2005;Suzuki and Bird, 2008;Law and Jacobsen, 2010) and loss of this modification is associated with transcriptional reactivation as well as increased mobilization of transposable elements (TEs; Slotkin and Martienssen, 2007). These observations likely reflect the ancestral role of cytosine methylation in the defence against invasive DNA. Methylation of repeat elements is also thought to have been exapted recurrently during eukaryotic evolution to exert other essential functions, notably in the epigenetic regulation of genes. Thus, genomic imprinting, which results in parent-of-origin-dependent expression, may have evolved in plants and mammals from situations in which methylation of repeat elements influences the activity of neighbouring genes (Barlow, 1993;M...

show abstract

Section: Variation In Rddm Strength and Paramutationmentioning

confidence: 79%

Section: Variation In Rddm Strength and Paramutationmentioning

confidence: 99%

Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

View full text Add to dashboard Cite

show abstract

“…The existing protocols for the last two methods cannot simply be transferred to plant tissues due to the special properties and unique chemical composition of plants. In this paper we provide a maize-specific 3C protocol that we recently developed and successfully applied 14 . Moreover, we present a general strategy to systematically optimize the protocol for other plants.…”

Section: Methods To Investigate Chromatin Interactionsmentioning

confidence: 99%

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

et al. 2009

Self Cite

View full text Add to dashboard Cite

“…The tandem repeats mediate enhancer activity that functions in cis to increase transcription from the b1 gene when in the B-I state (20), potentially through a long-distance looping mechanism because the tandem repeats interact with the transcription start site of the b1 gene differentially in B-I vs. B′ (23). The molecular nature of the genes required for paramutation strongly suggests that an RNA-dependent mechanism is critical for paramutation.…”

mentioning

confidence: 99%

“…This sequence is unique to this location within the maize genome, and both B-I and B′ carry seven tandem repeats, whereas alleles that do not undergo paramutation have a single copy of the repeat unit (20,21). B-I and B′ are epialleles; that is, they have identical DNA sequences but show distinct patterns of DNA methylation and chromatin structure within the tandem repeats (20,(22)(23)(24). Generation of an allelic series with different numbers of repeats demonstrated that multiple repeats are required for paramutation (20).…”

mentioning

confidence: 99%

RNA-mediated trans -communication can establish paramutation at the b1 locus in maize

Arteaga-Vázquez

Сидоренко

Rabanal

et al. 2010

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

View full text Add to dashboard Cite

Paramutation is the epigenetic transfer of information between alleles that leads to the heritable change of expression of one allele. Paramutation at the b1 locus in maize requires seven noncoding tandem repeat (b1TR) sequences located ∼100 kb upstream of the transcription start site of b1, and mutations in several genes required for paramutation implicate an RNA-mediated mechanism. The mediator of paramutation (mop1) gene, which encodes a protein closely related to RNA-dependent RNA polymerases, is absolutely required for paramutation. Herein, we investigate the potential function of mop1 and the siRNAs that are produced from the b1TR sequences. Production of siRNAs from the b1TR sequences depends on a functional mop1 gene, but transcription of the repeats is not dependent on mop1. Further nuclear transcription assays suggest that the b1TR sequences are likely transcribed predominantly by RNA polymerase II. To address whether production of b1TR-siRNAs correlated with paramutation, we examined siRNA production in alleles that cannot undergo paramutation. Alleles that cannot participate in paramutation also produce b1TR-siRNAs, suggesting that b1TR-siRNAs are not sufficient for paramutation in the tissues analyzed. However, when b1TR-siRNAs are produced from a transgene expressing a hairpin RNA, b1 paramutation can be recapitulated. We hypothesize that either the b1TR-siRNAs or the dsRNA template mediates the trans-communication between the alleles that establishes paramutation. In addition, we uncovered a role for mop1 in the biogenesis of a subset of microRNAs (miRNAs) and show that it functions at the level of production of the primary miRNA transcripts.interchromosomal | transfer | epigenetic | information | trans-generational

show abstract

Tissue- and Expression Level–Specific Chromatin Looping at Maizeb1Epialleles

Cited by 128 publications

References 45 publications

Repeat elements and the Arabidopsis DNA methylation landscape

Repeat elements and the Arabidopsis DNA methylation landscape

Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)

RNA-mediated trans -communication can establish paramutation at the b1 locus in maize

Contact Info

Product

Resources

About