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Vicki L Chandler - One of the best experts on this subject based on the ideXlab platform.
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specific tandem repeats are sufficient for Paramutation induced trans generational silencing
PLOS Genetics, 2013Co-Authors: Christiane Belele, Lyudmila Sidorenko, Maike Stam, Rechien Bader, Mario A Arteagavazquez, Vicki L ChandlerAbstract:Paramutation is a well-studied epigenetic phenomenon in which trans communication between two different alleles leads to meiotically heritable transcriptional silencing of one of the alleles. Paramutation at the b1 locus involves RNA-mediated transcriptional silencing and requires specific tandem repeats that generate siRNAs. This study addressed three important questions: 1) are the tandem repeats sufficient for Paramutation, 2) do they need to be in an allelic position to mediate Paramutation, and 3) is there an association between the ability to mediate Paramutation and repeat DNA methylation levels? Paramutation was achieved using multiple transgenes containing the b1 tandem repeats, including events with tandem repeats of only one half of the repeat unit (413 bp), demonstrating that these sequences are sufficient for Paramutation and an allelic position is not required for the repeats to communicate. Furthermore, the transgenic tandem repeats increased the expression of a reporter gene in maize, demonstrating the repeats contain transcriptional regulatory sequences. Transgene-mediated Paramutation required the mediator of Paramutation1 gene, which is necessary for endogenous Paramutation, suggesting endogenous and transgene-mediated Paramutation both require an RNA-mediated transcriptional silencing pathway. While all tested repeat transgenes produced small interfering RNAs (siRNAs), not all transgenes induced Paramutation suggesting that, as with endogenous alleles, siRNA production is not sufficient for Paramutation. The repeat transgene-induced silencing was less efficiently transmitted than silencing induced by the repeats of endogenous b1 alleles, which is always 100% efficient. The variability in the strength of the repeat transgene-induced silencing enabled testing whether the extent of DNA methylation within the repeats correlated with differences in efficiency of Paramutation. Transgene-induced Paramutation does not require extensive DNA methylation within the transgene. However, increased DNA methylation within the endogenous b1 repeats after transgene-induced Paramutation was associated with stronger silencing of the endogenous allele.
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maize unstable factor for orange1 is required for maintaining silencing associated with Paramutation at the pericarp color1 and booster1 loci
PLOS Genetics, 2012Co-Authors: Rajandeep S Sekhon, Lyudmila Sidorenko, Vicki L Chandler, Pohao Wang, Surinder ChopraAbstract:To understand the molecular mechanisms underlying Paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining Paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1 mutation disrupted silencing associated with Paramutation at both p1 and b1. The level of up regulation achieved at b1 was lower than that at p1, suggesting differences in the role Ufo1-1 plays at these loci. We characterized the interaction of Ufo1-1 with two silenced p1 epialleles, P1-rr′ and P1-prTP, that were derived from a common P1-rr ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; P1-rr′ is paramutagenic to P1-rr, while P1-prTP is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for Paramutation; P1-rr′ exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while P1-prTP was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the Ufo1-1 background; however, reactivation of P1-rr′ was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated P1-prTP was not affected. Interestingly, Ufo1-1–mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the Ufo1-1–reactivated p1 alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic p1 alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.
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Paramutation s properties and puzzles
Science, 2010Co-Authors: Vicki L ChandlerAbstract:Paramutation refers to the process by which homologous DNA sequences communicate in trans to establish meiotically heritable expression states. Although mechanisms are unknown, current data are consistent with the hypothesis that the establishment and heritable transmission of specific chromatin states underlies Paramutation. Transcribed, noncoding tandem repeats and proteins implicated in RNA-directed transcriptional silencing in plants and yeast are required for Paramutation, yet the specific molecules mediating heritable silencing remain to be determined.
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rna mediated trans communication can establish Paramutation at the b1 locus in maize
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Mario A Arteagavazquez, Lyudmila Sidorenko, Blake C Meyers, Fernando A Rabanal, Roli Shrivistava, Kan Nobuta, Pamela J Green, Vicki L ChandlerAbstract: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.
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Paramutation in maize rna mediated trans generational gene silencing
Current Opinion in Genetics & Development, 2010Co-Authors: Mario A Arteagavazquez, Vicki L ChandlerAbstract:Paramutation involves trans-interactions between alleles or homologous sequences that establish distinct gene expression states that are heritable for generations. It was first described in maize by Alexander Brink in the 1950s, with his studies of the red1 (r1) locus. Since that time, Paramutation-like phenomena have been reported in other maize genes, other plants, fungi, and animals. Paramutation can occur between endogenous genes, two transgenes or an endogenous gene, and transgene. Recent results indicate that Paramutation involves RNA-mediated heritable chromatin changes and a number of genes implicated in RNAi pathways. However, not all aspects of Paramutation can be explained by known mechanisms of RNAi-mediated transcriptional silencing.
Minoo Rassoulzadegan - One of the best experts on this subject based on the ideXlab platform.
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A new Paramutation-like example at the Delta gene of Drosophila
PLoS ONE, 2017Co-Authors: Maria Capovilla, Alain Robichon, Minoo RassoulzadeganAbstract:The hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate Paramutation in Drosophila, we used the P{ry+t7.2 = PZ}Dl05151 P-element insertion in the Drosophila melanogaster genome that causes a dominant visible phenotype: the presence of characteristic extra-veins in the fly wings. This extra-vein phenotype presents variable expressivity and incomplete penetrance. The insert is a PZ element located 680 bp upstream from the ATG of the Delta (Dl) gene, encoding the Notch ligand involved in wing vein development, and acts as a null allele. In the G2 offspring from a cross between the heterozygous transgenic stock and wild-type flies, we observed the transmission of the extra-vein phenotype to wild-type flies without the transgene, independently of gender and across many generations. This is a “Paramutation-like” example in the fly: the heritable transmission of a phenotypic change not linked to a classical genetic mutation. A “paramutagenic” allele in heterozygotes transmits the phenotype of the heterozygotes to the wild-type allele (“paramutant”) in a stable manner through generations. Distinct from Paramutation events so far described in Drosophila, here we deal with a dominant effect on a single gene involving variable hereditary signals.
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From Paramutation to human disease: RNA-mediated heredity.
Seminars in Cell and Developmental Biology, 2015Co-Authors: Minoo Rassoulzadegan, François CuzinAbstract:Epigenetic variation, a stable alteration in gene expression, occurs at multiple moments during development. Several instances of non-Mendelian transmission to the progenies modes are very intriguing. Studies of the mode of hereditary transmission revealed in a series of such cases a role of noncoding RNA molecules as inducers. While still an enigmatic mechanism, emerging models pinpoint to a more general roles of these variations, initiated as a response to genetic and environmental variation. Here we compare the known modes of transgenerational epigenetic variation in mice and humans.
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non mendelian epigenetic heredity gametic rnas as epigenetic regulators and transgenerational signals
Essays in Biochemistry, 2010Co-Authors: Minoo Rassoulzadegan, François CuzinAbstract:Inheritance of epigenetic variations may account for a significant part of heritability in human and in mammalian models. Heritable epigenetic variations were reported in plants under the name 'Paramutation' more than 50 years ago. Reports by E. Whitelaw and her colleagues and by our laboratory now describe a variety of situations resulting in epigenetic inheritance in mouse systems. In the three cases that we have analysed, a transcriptional increase is initiated by RNAs related to the locus, either microRNAs or transcript fragments. RNAs carried by the spermatozoon appear as the transgenerational signals responsible for paternal transmission. Extension from mouse models to human heredity, obviously speculative at present, is encouraged by the high load of RNA in human sperm.
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the mir 124 sox9 Paramutation rna mediated epigenetic control of embryonic and adult growth
Journal of Cell Science, 2009Co-Authors: Valérie Grandjean, François Cuzin, Pierre Gounon, Nicole Wagner, Luc Martin, Kay D Wagner, Florence Bernex, Minoo RassoulzadeganAbstract:Grandjean, V. et al. 2009. Development doi:10.1242/dev.041061[OpenUrl][1][Abstract/FREE Full Text][2] [1]: {openurl}?query=rft.jtitle%253DDevelopment%26rft.stitle%253DDevelopment%26rft.issn%253D0950-1991%26rft.aulast%253DGrandjean%26rft.auinit1%253DV.%26rft.volume%253D136%26rft.issue%253D21%26rft.
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The miR-124-Sox9 Paramutation: RNA-mediated epigenetic control of embryonic and adult growth
Development (Cambridge England), 2009Co-Authors: Valérie Grandjean, François Cuzin, Pierre Gounon, Nicole Wagner, Luc Martin, Kay D Wagner, Florence Bernex, Minoo RassoulzadeganAbstract:The size of the mammalian body is determined by genetic and environmental factors differentially modulating pre- and postnatal growth. We now report a control of growth acting in the mouse from the first cleavages to the postnatal stages. It was evidenced by a hereditary epigenetic modification (Paramutation) created by injection of a miR-124 microRNA into fertilized eggs. From the blastocyst to the adult, mouse pups born after microinjection of this miRNA showed a 30% increase in size. At the blastocyst stage, frequent duplication of the inner cell mass resulted in twin pregnancies. A role of sperm RNA as a transgenerational signal was confirmed by the giant phenotype of the progeny of transgenic males expressing miR-124 during spermiogenesis. In E2.5 to E8.5 embryos, increased levels of several transcripts with sequence homology to the microRNA were noted, including those of Sox9, a gene known for its crucial role in the progenitors of several adult tissues. A role in embryonic growth was confirmed by the large size of embryos expressing a Sox9 DNA transgene. Increased expression in the paramutants was not related to a change in miR-124 expression, but to the establishment of a distinct, heritable chromatin structure in the promoter region of Sox9. While the heritability of body size is not readily accounted for by Mendelian genetics, our results suggest the alternate model of RNA-mediated heritable epigenetic modifications.
Jay B Hollick - One of the best experts on this subject based on the ideXlab platform.
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locus specific Paramutation in zea mays is maintained by a pickle like chromodomain helicase dna binding 3 protein controlling development and male gametophyte function
PLOS Genetics, 2020Co-Authors: Natalie C Deans, Brian Giacopelli, Jay B HollickAbstract:Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of Paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as another component maintaining both pl1 Paramutation and normal somatic development but without affecting overall small RNA biogenesis. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two Paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also helps maintain meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the Paramutation process.
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Paramutation and related phenomena in diverse species
Nature Reviews Genetics, 2017Co-Authors: Jay B HollickAbstract:Paramutation describes a process that results in heritable epigenetic changes of gene regulation and trans-homologue interactions. Recent discoveries in model organisms have highlighted roles for the respective nuclear systems that regulate transposons via small RNA molecules both for Paramutation and for defining transgenerational inheritance. Differences between plants and animals may influence specific transmission behaviours but the involvement of small RNA-based mechanisms identifies a unifying eukaryotic theme. These mechanisms that specify heritable epigenetic information represent genetic systems adjunct to DNA sequences that contribute to phenotypic diversity.
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Paramutation in maize and related behaviors in metazoans.
Seminars in cell & developmental biology, 2015Co-Authors: Janelle Gabriel, Jay B HollickAbstract:Paramutation refers to both the process and results of trans-homolog interactions causing heritable changes in both gene regulation and silencing abilities. Originally described in plants, Paramutation-like behaviors have now been reported in model metazoans. Here we detail our current understanding of the Paramutation mechanism as defined in Zea mays and compare this paradigm to these metazoan examples. Experimental results implicate functional roles of small RNAs in all these model organisms that highlight a diversity of mechanisms by which these molecules specify meiotically heritable regulatory information in the eukarya.
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trans homolog interactions facilitating Paramutation in maize
Plant Physiology, 2015Co-Authors: Brian Giacopelli, Jay B HollickAbstract:Paramutations represent locus-specific trans-homolog interactions affecting the heritable silencing properties of endogenous alleles. Although examples of Paramutation are well studied in maize (Zea mays), the responsible mechanisms remain unclear. Genetic analyses indicate roles for plant-specific DNA-dependent RNA polymerases that generate small RNAs, and current working models hypothesize that these small RNAs direct heritable changes at sequences often acting as transcriptional enhancers. Several studies have defined specific sequences that mediate Paramutation behaviors, and recent results identify a diversity of DNA-dependent RNA polymerase complexes operating in maize. Other reports ascribe broader roles for some of these complexes in normal genome function. This review highlights recent research to understand the molecular mechanisms of Paramutation and examines evidence relevant to small RNA-based modes of transgenerational epigenetic inheritance.
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Paramutation a trans homolog interaction affecting heritable gene regulation
Current Opinion in Plant Biology, 2012Co-Authors: Jay B HollickAbstract:Paramutation describes both the process and results of trans-sensing between chromosomes that causes specific heritable changes in gene regulation. RNA molecules are implicated in mediating similar events in maize, mouse, and Drosophila. Changes in both small RNA profiles and cytosine methylation patterns in Arabidopsis hybrids represent a potential molecular equivalent to the interactions responsible for Paramutations. Despite a seemingly unifying feature of RNA-directed changes, both recent and historical works show that Paramutations in maize require plant-specific proteins and lack expected hallmarks of a trans-effect mediated solely by RNAs. Recent examples of nearby transposons affecting RNA polymerase II functions lead to an opinion that Paramutations represent an emergent property of the transcriptional dynamics ongoing in plant genomes between repetitious features and nearby genes.
François Cuzin - One of the best experts on this subject based on the ideXlab platform.
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From Paramutation to human disease: RNA-mediated heredity.
Seminars in Cell and Developmental Biology, 2015Co-Authors: Minoo Rassoulzadegan, François CuzinAbstract:Epigenetic variation, a stable alteration in gene expression, occurs at multiple moments during development. Several instances of non-Mendelian transmission to the progenies modes are very intriguing. Studies of the mode of hereditary transmission revealed in a series of such cases a role of noncoding RNA molecules as inducers. While still an enigmatic mechanism, emerging models pinpoint to a more general roles of these variations, initiated as a response to genetic and environmental variation. Here we compare the known modes of transgenerational epigenetic variation in mice and humans.
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rna mediated epigenetic heredity requires the cytosine methyltransferase dnmt2
PLOS Genetics, 2013Co-Authors: Jafar Kiani, Hossein Ghanbarian, Valérie Grandjean, Francesca Tuorto, Reinhard Liebers, Frank Lyko, François CuzinAbstract:RNA–mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these Paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and the modulation of the Sox9 gene, resulting in an overgrowth phenotype. We now report that expression of the Dnmt2 RNA methyltransferase is required for the establishment and hereditary maintenance of both Paramutations. Our data show that the Kit paramutant phenotype was not transmitted to the progeny of Dnmt2−/− mice and that the Sox9 Paramutation was also not established in Dnmt2−/− embryos. Similarly, RNA from Dnmt2-negative Kit heterozygotes did not induce the paramutant phenotype when microinjected into Dnmt2-deficient fertilized eggs and microinjection of the miR-124 microRNA failed to induce the characteristic giant phenotype. In agreement with an RNA–mediated mechanism of inheritance, no change was observed in the DNA methylation profiles of the Kit locus between the wild-type and paramutant mice. RNA bisulfite sequencing confirmed Dnmt2-dependent tRNA methylation in mouse sperm and also indicated Dnmt2-dependent cytosine methylation in Kit RNA in paramutant embryos. Together, these findings uncover a novel function of Dnmt2 in RNA–mediated epigenetic heredity.
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non mendelian epigenetic heredity gametic rnas as epigenetic regulators and transgenerational signals
Essays in Biochemistry, 2010Co-Authors: Minoo Rassoulzadegan, François CuzinAbstract:Inheritance of epigenetic variations may account for a significant part of heritability in human and in mammalian models. Heritable epigenetic variations were reported in plants under the name 'Paramutation' more than 50 years ago. Reports by E. Whitelaw and her colleagues and by our laboratory now describe a variety of situations resulting in epigenetic inheritance in mouse systems. In the three cases that we have analysed, a transcriptional increase is initiated by RNAs related to the locus, either microRNAs or transcript fragments. RNAs carried by the spermatozoon appear as the transgenerational signals responsible for paternal transmission. Extension from mouse models to human heredity, obviously speculative at present, is encouraged by the high load of RNA in human sperm.
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the mir 124 sox9 Paramutation rna mediated epigenetic control of embryonic and adult growth
Journal of Cell Science, 2009Co-Authors: Valérie Grandjean, François Cuzin, Pierre Gounon, Nicole Wagner, Luc Martin, Kay D Wagner, Florence Bernex, Minoo RassoulzadeganAbstract:Grandjean, V. et al. 2009. Development doi:10.1242/dev.041061[OpenUrl][1][Abstract/FREE Full Text][2] [1]: {openurl}?query=rft.jtitle%253DDevelopment%26rft.stitle%253DDevelopment%26rft.issn%253D0950-1991%26rft.aulast%253DGrandjean%26rft.auinit1%253DV.%26rft.volume%253D136%26rft.issue%253D21%26rft.
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The miR-124-Sox9 Paramutation: RNA-mediated epigenetic control of embryonic and adult growth
Development (Cambridge England), 2009Co-Authors: Valérie Grandjean, François Cuzin, Pierre Gounon, Nicole Wagner, Luc Martin, Kay D Wagner, Florence Bernex, Minoo RassoulzadeganAbstract:The size of the mammalian body is determined by genetic and environmental factors differentially modulating pre- and postnatal growth. We now report a control of growth acting in the mouse from the first cleavages to the postnatal stages. It was evidenced by a hereditary epigenetic modification (Paramutation) created by injection of a miR-124 microRNA into fertilized eggs. From the blastocyst to the adult, mouse pups born after microinjection of this miRNA showed a 30% increase in size. At the blastocyst stage, frequent duplication of the inner cell mass resulted in twin pregnancies. A role of sperm RNA as a transgenerational signal was confirmed by the giant phenotype of the progeny of transgenic males expressing miR-124 during spermiogenesis. In E2.5 to E8.5 embryos, increased levels of several transcripts with sequence homology to the microRNA were noted, including those of Sox9, a gene known for its crucial role in the progenitors of several adult tissues. A role in embryonic growth was confirmed by the large size of embryos expressing a Sox9 DNA transgene. Increased expression in the paramutants was not related to a change in miR-124 expression, but to the establishment of a distinct, heritable chromatin structure in the promoter region of Sox9. While the heritability of body size is not readily accounted for by Mendelian genetics, our results suggest the alternate model of RNA-mediated heritable epigenetic modifications.
Lyudmila Sidorenko - One of the best experts on this subject based on the ideXlab platform.
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functional diversification of maize rna polymerase iv and v subtypes via alternative catalytic subunits
Cell Reports, 2014Co-Authors: Lyudmila Sidorenko, Jeremy R Haag, Brent Browertoland, Elysia K Krieger, Carrie D Nicora, Angela D Norbeck, Andre Irsigler, Huachun Larue, Jan BrzeskiAbstract:Summary Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and Paramutation, yields at least two subtypes of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between Paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis .
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specific tandem repeats are sufficient for Paramutation induced trans generational silencing
PLOS Genetics, 2013Co-Authors: Christiane Belele, Lyudmila Sidorenko, Maike Stam, Rechien Bader, Mario A Arteagavazquez, Vicki L ChandlerAbstract:Paramutation is a well-studied epigenetic phenomenon in which trans communication between two different alleles leads to meiotically heritable transcriptional silencing of one of the alleles. Paramutation at the b1 locus involves RNA-mediated transcriptional silencing and requires specific tandem repeats that generate siRNAs. This study addressed three important questions: 1) are the tandem repeats sufficient for Paramutation, 2) do they need to be in an allelic position to mediate Paramutation, and 3) is there an association between the ability to mediate Paramutation and repeat DNA methylation levels? Paramutation was achieved using multiple transgenes containing the b1 tandem repeats, including events with tandem repeats of only one half of the repeat unit (413 bp), demonstrating that these sequences are sufficient for Paramutation and an allelic position is not required for the repeats to communicate. Furthermore, the transgenic tandem repeats increased the expression of a reporter gene in maize, demonstrating the repeats contain transcriptional regulatory sequences. Transgene-mediated Paramutation required the mediator of Paramutation1 gene, which is necessary for endogenous Paramutation, suggesting endogenous and transgene-mediated Paramutation both require an RNA-mediated transcriptional silencing pathway. While all tested repeat transgenes produced small interfering RNAs (siRNAs), not all transgenes induced Paramutation suggesting that, as with endogenous alleles, siRNA production is not sufficient for Paramutation. The repeat transgene-induced silencing was less efficiently transmitted than silencing induced by the repeats of endogenous b1 alleles, which is always 100% efficient. The variability in the strength of the repeat transgene-induced silencing enabled testing whether the extent of DNA methylation within the repeats correlated with differences in efficiency of Paramutation. Transgene-induced Paramutation does not require extensive DNA methylation within the transgene. However, increased DNA methylation within the endogenous b1 repeats after transgene-induced Paramutation was associated with stronger silencing of the endogenous allele.
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maize unstable factor for orange1 is required for maintaining silencing associated with Paramutation at the pericarp color1 and booster1 loci
PLOS Genetics, 2012Co-Authors: Rajandeep S Sekhon, Lyudmila Sidorenko, Vicki L Chandler, Pohao Wang, Surinder ChopraAbstract:To understand the molecular mechanisms underlying Paramutation, we examined the role of Unstable factor for orange1 (Ufo1) in maintaining Paramutation at the maize pericarp color1 (p1) and booster1 (b1) loci. Genetic tests revealed that the Ufo1-1 mutation disrupted silencing associated with Paramutation at both p1 and b1. The level of up regulation achieved at b1 was lower than that at p1, suggesting differences in the role Ufo1-1 plays at these loci. We characterized the interaction of Ufo1-1 with two silenced p1 epialleles, P1-rr′ and P1-prTP, that were derived from a common P1-rr ancestor. Both alleles are phenotypically indistinguishable, but differ in their paramutagenic activity; P1-rr′ is paramutagenic to P1-rr, while P1-prTP is non-paramutagenic. Analysis of cytosine methylation revealed striking differences within an enhancer fragment that is required for Paramutation; P1-rr′ exhibited increased methylation at symmetric (CG and CHG) and asymmetric (CHH) sites, while P1-prTP was methylated only at symmetric sites. Both silenced alleles had higher levels of dimethylation of lysine 9 on histone 3 (H3K9me2), an epigenetic mark of silent chromatin, in the enhancer region. Both epialleles were reactivated in the Ufo1-1 background; however, reactivation of P1-rr′ was associated with dramatic loss of symmetric and asymmetric cytosine methylation in the enhancer, while methylation of up-regulated P1-prTP was not affected. Interestingly, Ufo1-1–mediated reactivation of both alleles was accompanied with loss of H3K9me2 mark from the enhancer region. Therefore, while earlier studies have shown correlation between H3K9me2 and DNA methylation, our study shows that these two epigenetic marks are uncoupled in the Ufo1-1–reactivated p1 alleles. Furthermore, while CHH methylation at the enhancer region appears to be the major distinguishing mark between paramutagenic and non-paramutagenic p1 alleles, H3K9me2 mark appears to be important for maintaining epigenetic silencing.
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rna mediated trans communication can establish Paramutation at the b1 locus in maize
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Mario A Arteagavazquez, Lyudmila Sidorenko, Blake C Meyers, Fernando A Rabanal, Roli Shrivistava, Kan Nobuta, Pamela J Green, Vicki L ChandlerAbstract: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.
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rna dependent rna polymerase is required for enhancer mediated transcriptional silencing associated with Paramutation at the maize p1 gene
Genetics, 2008Co-Authors: Lyudmila Sidorenko, Vicki L ChandlerAbstract:Paramutation is the ability of an endogenous gene or a transgene to heritably silence another closely related allele or gene. At the maize p1 (pericarp color1) gene, Paramutation is associated with decreases in transcript levels and reduced pigmentation of the endogenous allele that normally specifies red seed coat (pericarp) and cob pigmentation. Herein we demonstrate that this silencing occurs at the transcriptional level and that a specific enhancer fragment from p1 is sufficient to induce all aspects of Paramutation. Further, we demonstrate that a mutation in the mop1 gene (mediator of Paramutation1), which encodes a RNA-dependent RNA polymerase, is absolutely required for establishing the silencing associated with p1 Paramutation. In contrast to its effects on other Paramutation loci, the mop1 mutation does not immediately reactivate a previously silenced allele; several generations in the presence of the mop1 mutation are required. In addition, the mop1 mutation was also able to release tissue-specific silencing of another p1 allele that does not participate in Paramutation, but does contain a tandem repeated structure and is likely regulated through epigenetic mechanisms. These results demonstrate that RNA-mediated gene-silencing mechanisms play key roles in p1 Paramutation and the spectrum of roles for MOP1 is broadened to include tissue-specific expression patterns.