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1.
BMC Plant Biol ; 24(1): 405, 2024 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-38750420

RESUMEN

BACKGROUND: In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction. RESULTS: Our genome-wide study provides evidence for stress memory acquisition and maintenance in F. vesca. We found that specific DNA methylation marks or epimutations are stably transmitted over at least three asexual generations. Some of the epimutations were associated with transcriptional changes after heat stress. CONCLUSION: Our findings show that the strawberry methylome and transcriptome respond with a high level of flexibility to heat stress. Notably, independent plants acquired the same epimutations and those were inherited by their asexual progenies. Overall, the asexual progenies can retain some information in the genome of past stresses encountered by their progenitors. This molecular memory, also documented at the transcriptional level, might be involved in functional plasticity and stress adaptation. Finally, these findings may contribute to novel breeding approaches for climate-ready plants.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Fragaria , Respuesta al Choque Térmico , Transcriptoma , Fragaria/genética , Fragaria/fisiología , Respuesta al Choque Térmico/genética , Epigenómica , Regulación de la Expresión Génica de las Plantas , Reproducción Asexuada/genética
2.
Nucleic Acids Res ; 49(18): 10431-10447, 2021 10 11.
Artículo en Inglés | MEDLINE | ID: mdl-34551439

RESUMEN

Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.


Asunto(s)
Arabidopsis/genética , Respuesta al Choque Térmico/genética , Retroelementos , Transcriptoma , Arabidopsis/efectos de los fármacos , Arabidopsis/metabolismo , Proteínas de Arabidopsis/análisis , Citidina/análogos & derivados , Citidina/toxicidad , Epigénesis Genética , Exones , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Código de Histonas , Histonas/análisis , Fenotipo
3.
PLoS Genet ; 16(4): e1008324, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-32287271

RESUMEN

Transposable elements (TEs) are DNA repeats that must remain silenced to ensure cell integrity. Several epigenetic pathways including DNA methylation and histone modifications are involved in the silencing of TEs, and in the regulation of gene expression. In Arabidopsis thaliana, the TE-derived plant mobile domain (PMD) proteins have been involved in TE silencing, genome stability, and control of developmental processes. Using a forward genetic screen, we found that the PMD protein MAINTENANCE OF MERISTEMS (MAIN) acts synergistically and redundantly with DNA methylation to silence TEs. We found that MAIN and its close homolog MAIN-LIKE 1 (MAIL1) interact together, as well as with the phosphoprotein phosphatase (PPP) PP7-like (PP7L). Remarkably, main, mail1, pp7l single and mail1 pp7l double mutants display similar developmental phenotypes, and share common subsets of upregulated TEs and misregulated genes. Finally, phylogenetic analyses of PMD and PP7-type PPP domains among the Eudicot lineage suggest neo-association processes between the two protein domains to potentially generate new protein function. We propose that, through this interaction, the PMD and PPP domains may constitute a functional protein module required for the proper expression of a common set of genes, and for silencing of TEs.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Elementos Transponibles de ADN/genética , Regulación de la Expresión Génica de las Plantas , Silenciador del Gen , Proteínas Nucleares/metabolismo , Fosfoproteínas Fosfatasas/metabolismo , Arabidopsis/crecimiento & desarrollo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Metilación de ADN , Epigénesis Genética , Heterocromatina/metabolismo , Mutación , Proteínas Nucleares/genética , Fosfoproteínas Fosfatasas/genética , Unión Proteica , Dominios Proteicos , Proteínas Represoras/genética , Proteínas Represoras/metabolismo
4.
New Phytol ; 236(1): 182-194, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-35715973

RESUMEN

Eukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognised as a source of genetic diversity and powerful drivers of evolution. However, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scarce. We exposed Arabidopsis thaliana high-copy TE lines (hcLines) with up to c. eight-fold increased copy numbers of the heat-responsive ONSEN TE to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis, plant size and water consumption. Overall, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in A. thaliana. This is one of the rare empirical examples substantiating the adaptive potential of mobilised stress-responsive TEs in eukaryotes. Our work demonstrates the potential of TE-mediated loss-of-function mutations in stress adaptation.


Asunto(s)
Arabidopsis , Adaptación Fisiológica/genética , Arabidopsis/genética , Elementos Transponibles de ADN/genética , Sequías , Evolución Molecular , Calor
5.
Nucleic Acids Res ; 47(17): 9037-9052, 2019 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-31372633

RESUMEN

RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV's largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , ARN Polimerasas Dirigidas por ADN/genética , Regulación de la Expresión Génica de las Plantas , Secuencias de Aminoácidos , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Metilación de ADN/genética , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/metabolismo , Silenciador del Gen , Genoma de Planta , Plantas Modificadas Genéticamente , Dominios Proteicos/genética , ARN Interferente Pequeño/biosíntesis , ARN Interferente Pequeño/genética , ARN Polimerasa Dependiente del ARN/metabolismo , Retroelementos/genética
6.
Plant J ; 98(4): 697-713, 2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-30715761

RESUMEN

Drought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large-scale circRNA profiling identified 2174 and 1354 high-confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought-associated circRNA-hosting genes were involved in conserved or species-specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA-hosting genes were enriched for single nucleotide polymorphisms (SNPs) associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought-tolerant maize. Additionally, the expression levels of circRNAs derived from drought-responsible genes encoding calcium-dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward-rectifying K+ -channel) were hypersensitive to abscisic acid, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidence highlighting the universal molecular mechanisms involved in plant drought tolerance.


Asunto(s)
Arabidopsis/metabolismo , ARN Circular/metabolismo , ARN de Planta/metabolismo , Estrés Fisiológico/fisiología , Zea mays/metabolismo , Aclimatación/genética , Aclimatación/fisiología , Arabidopsis/genética , Cruzamiento , Sequías , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Malondialdehído/metabolismo , Oxidorreductasas/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Prolina/metabolismo , ARN Circular/genética , ARN de Planta/genética , Plantones , Análisis de Secuencia de ARN , Estrés Fisiológico/genética , Zea mays/genética
7.
Plant Mol Biol ; 100(1-2): 199-214, 2019 May.
Artículo en Inglés | MEDLINE | ID: mdl-30868544

RESUMEN

KEY MESSAGE: Here we demonstrate that the APUM9 RNA-binding protein and its co-factors play a role in mRNA destabilization and how this activity might regulate early plant development. APUM9 is a conserved PUF RNA-binding protein (RBP) under complex transcriptional control mediated by a transposable element (TE) that restricts its expression in Arabidopsis. Currently, little is known about the functional and mechanistic details of the plant PUF regulatory system and the biological relevance of the TE-mediated repression of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here, that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunit of the decapping complex and DCP2 overexpression induces rapid decay of APUM9 targeted mRNAs. We show that APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated control of APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.


Asunto(s)
Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Secuencia Conservada , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Adaptación Fisiológica , Arabidopsis/fisiología , Dominio Catalítico , Elementos Transponibles de ADN/genética , Desarrollo de la Planta , Latencia en las Plantas , Unión Proteica , Dominios Proteicos , Estabilidad del ARN , ARN Mensajero/genética , ARN Mensajero/metabolismo , Semillas/metabolismo , Estrés Fisiológico
8.
J Exp Bot ; 70(4): 1349-1365, 2019 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-30715439

RESUMEN

Small secreted peptides are important players in plant development and stress response. Using a targeted in silico approach, we identified a family of 14 Arabidopsis genes encoding precursors of serine-rich endogenous peptides (PROSCOOP). Transcriptomic analyses revealed that one member of this family, PROSCOOP12, is involved in processes linked to biotic and oxidative stress as well as root growth. Plants defective in this gene were less susceptible to Erwinia amylovora infection and showed an enhanced root growth phenotype. In PROSCOOP12 we identified a conserved motif potentially coding for a small secreted peptide. Exogenous application of synthetic SCOOP12 peptide induces various defense responses in Arabidopsis. Our findings show that SCOOP12 has numerous properties of phytocytokines, activates the phospholipid signaling pathway, regulates reactive oxygen species response, and is perceived in a BAK1 co-receptor-dependent manner.


Asunto(s)
Proteínas de Arabidopsis/fisiología , Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas/inmunología , Genes de Plantas , Péptidos y Proteínas de Señalización Intercelular/fisiología , Familia de Multigenes , Raíces de Plantas/crecimiento & desarrollo , Arabidopsis/crecimiento & desarrollo , Arabidopsis/inmunología , Proteínas de Arabidopsis/genética , Péptidos y Proteínas de Señalización Intercelular/genética , Raíces de Plantas/genética , Transducción de Señal
10.
Ecol Lett ; 20(12): 1576-1590, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-29027325

RESUMEN

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.


Asunto(s)
Ecología , Epigénesis Genética , Plantas , Metilación de ADN , Ecosistema
11.
Nature ; 472(7341): 115-9, 2011 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-21399627

RESUMEN

Eukaryotic genomes consist to a significant extent of retrotransposons that are suppressed by host epigenetic mechanisms, preventing their uncontrolled propagation. However, it is not clear how this is achieved. Here we show that in Arabidopsis seedlings subjected to heat stress, a copia-type retrotransposon named ONSEN (Japanese 'hot spring') not only became transcriptionally active but also synthesized extrachromosomal DNA copies. Heat-induced ONSEN accumulation was stimulated in mutants impaired in the biogenesis of small interfering RNAs (siRNAs); however, there was no evidence of transposition occurring in vegetative tissues. After stress, both ONSEN transcripts and extrachromosomal DNA gradually decayed and were no longer detected after 20-30 days. Surprisingly, a high frequency of new ONSEN insertions was observed in the progeny of stressed plants deficient in siRNAs. Insertion patterns revealed that this transgenerational retrotransposition occurred during flower development and before gametogenesis. Therefore in plants with compromised siRNA biogenesis, memory of stress was maintained throughout development, priming ONSEN to transpose during differentiation of generative organs. Retrotransposition was not observed in the progeny of wild-type plants subjected to stress or in non-stressed mutant controls, pointing to a crucial role of the siRNA pathway in restricting retrotransposition triggered by environmental stress. Finally, we found that natural and experimentally induced variants in ONSEN insertions confer heat responsiveness to nearby genes, and therefore mobility bursts may generate novel, stress-responsive regulatory gene networks.


Asunto(s)
Arabidopsis/genética , Arabidopsis/fisiología , Respuesta al Choque Térmico , ARN de Planta/genética , ARN Interferente Pequeño/genética , Retroelementos/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Cromosomas de las Plantas , ADN de Plantas/genética , Regulación de la Expresión Génica de las Plantas/genética , Redes Reguladoras de Genes/genética , Genes de Plantas/genética , Respuesta al Choque Térmico/genética , Modelos Genéticos , Mutagénesis Insercional/genética , Plantones/genética , Transcripción Genética/genética
12.
Genes Dev ; 23(8): 939-50, 2009 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-19390088

RESUMEN

Transgenerational epigenetic inheritance has been defined by the study of relatively few loci. We examined a population of recombinant inbred lines with epigenetically mosaic chromosomes consisting of wild-type and CG methylation-depleted segments (epiRILs). Surprisingly, transposons that were immobile in the parental lines displayed stochastic movement in 28% of the epiRILs. Although analysis after eight generations of inbreeding, supported by genome-wide DNA methylation profiling, identified recombined parental chromosomal segments, these were interspersed with unexpectedly high frequencies of nonparental methylation polymorphism. Hence, epigenetic inheritance in hybrids derived from parents with divergent epigenomes permits long-lasting epi-allelic interactions that violate Mendelian expectations. Such persistently "unstable" epigenetic states complicate linkage-based epigenomic mapping. Thus, future epigenomic analyses should consider possible genetic instabilities and alternative mapping strategies.


Asunto(s)
Arabidopsis/genética , Arabidopsis/metabolismo , Metilación de ADN/genética , Elementos Transponibles de ADN/genética , Epigénesis Genética/genética , Genoma de Planta/genética , Inestabilidad Genómica/genética , Proteínas de Arabidopsis/genética , Mapeo Cromosómico , Cromosomas de las Plantas/genética , ADN (Citosina-5-)-Metiltransferasas/genética , Genes de Plantas/genética , Endogamia , Mosaicismo , Fenotipo , Recombinación Genética
13.
Plant Physiol ; 168(4): 1298-308, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-25918117

RESUMEN

To investigate the role of chromatin regulators in patterning gene expression, we employed a unique epigenetically controlled and highly tissue-specific green fluorescent protein reporter line in Arabidopsis (Arabidopsis thaliana). Using a combination of forward and reverse genetic approaches on this line, we show here that distinct epigenetic regulators are involved in silencing the transgene in different tissues. The forward genetic screen led to the identification of a novel HISTONE DEACETYLASE6 (HDA6) mutant allele (epigenetic control1, hda6-8). This allele differs from the previously reported alleles, as it did not affect DNA methylation and only had a very modest effect on the release of transposable elements and other heterochromatic transcripts. Overall, our data shows that HDA6 has at least two clearly separable activities in different genomic regions. In addition, we present an unexpected role for HDA6 in the control of DNA methylation at CG dinucleotides.


Asunto(s)
Arabidopsis/enzimología , Cromatina/genética , Epigénesis Genética , Regulación de la Expresión Génica de las Plantas , Acetilación , Alelos , Secuencia de Aminoácidos , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Metilación de ADN , Elementos Transponibles de ADN/genética , Eucromatina/genética , Expresión Génica , Silenciador del Gen , Histona Desacetilasas/genética , Histona Desacetilasas/metabolismo , Histonas/genética , Histonas/metabolismo , Especificidad de Órganos , Hojas de la Planta/enzimología , Hojas de la Planta/genética , Alineación de Secuencia , Transgenes
14.
Nature ; 461(7262): 427-30, 2009 Sep 17.
Artículo en Inglés | MEDLINE | ID: mdl-19734882

RESUMEN

Retrotransposons are mobile genetic elements that populate chromosomes, where the host largely controls their activities. In plants and mammals, retrotransposons are transcriptionally silenced by DNA methylation, which in Arabidopsis is propagated at CG dinucleotides by METHYLTRANSFERASE 1 (MET1). In met1 mutants, however, mobilization of retrotransposons is not observed, despite their transcriptional activation. A post-transcriptional mechanism therefore seems to be preventing retrotransposition. Here we show that a copia-type retrotransposon (Evadé, French for 'fugitive') evaded suppression of its movement during inbreeding of hybrid epigenomes consisting of met1- and wild-type-derived chromosomes. Evadé (EVD) reinsertions caused a series of developmental mutations that allowed its identification. Genetic testing of host control of the EVD life cycle showed that transcriptional suppression occurred by CG methylation supported by RNA-directed DNA methylation. On transcriptional reactivation, subsequent steps of the EVD cycle were inhibited by plant-specific RNA polymerase IV/V and the histone methyltransferase KRYPTONITE (KYP). Moreover, genome resequencing demonstrated retrotransposition of EVD but no other potentially active retroelements when this combination of epigenetic mechanisms was compromised. Our results demonstrate that epigenetic control of retrotransposons extends beyond transcriptional suppression and can be individualized for particular elements.


Asunto(s)
Arabidopsis/genética , Epigénesis Genética/genética , Mutagénesis Insercional/genética , Recombinación Genética/genética , Retroelementos/genética , Alelos , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , ADN (Citosina-5-)-Metiltransferasas/genética , Metilación de ADN , ARN Polimerasas Dirigidas por ADN/metabolismo , Silenciador del Gen , Genoma de Planta/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , Endogamia , Secuencias Repetidas Terminales/genética , Transcripción Genética/genética
15.
Proc Natl Acad Sci U S A ; 109(15): 5880-5, 2012 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-22451936

RESUMEN

During sexual reproduction, one-half of the genetic material is deposited in gametes, and a complete set of chromosomes is restored upon fertilization. Reduction of the genetic information before gametogenesis occurs in meiosis, when cross-overs (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it was postulated that DNA hypermethylation is inhibitory to COs. Here, when analyzing meiotic recombination in mutant plants with hypomethylated DNA, we observed unexpected and counterintuitive effects of DNA methylation losses on CO distribution. Recombination was further promoted in the hypomethylated chromosome arms while it was inhibited in heterochromatic regions encompassing pericentromeric DNA. Importantly, the total number of COs was not affected, implying that loss of DNA methylation led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influence recombination--whether directly in cis or indirectly in trans by changing expression of genes encoding recombination components--we analyzed CO distribution in wild-type lines with randomly scattered and well-mapped hypomethylated chromosomal segments. The results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. Because DNA methylation exhibits significant variation even within a single species, our results imply that it may influence the evolution of plant genomes through the control of meiotic recombination.


Asunto(s)
Arabidopsis/genética , Metilación de ADN/genética , Recombinación Genética , Arabidopsis/citología , Proteínas de Arabidopsis/genética , Cromosomas de las Plantas/genética , ADN (Citosina-5-)-Metiltransferasas/genética , Eucromatina/metabolismo , Heterocromatina/metabolismo , Endogamia , Meiosis/genética , Mutación/genética
16.
EMBO J ; 29(2): 340-51, 2010 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-19910926

RESUMEN

It is commonly observed that onset or release of transcriptional gene silencing (TGS) correlates with alteration of repressive epigenetic marks. The TGS regulator MOM1 in Arabidopsis is exceptional since it regulates transcription in intermediate heterochromatin with only minor changes in epigenetic marks. We have isolated an enhancer of the mom1 mutation that points towards regulatory interplay between MOM1 and RNA polymerase-V (Pol-V). Pol-V transcribes heterochromatic loci, which seems to be required for maintenance of their silencing; however, it is still not clear how Pol-V is targeted to heterochromatin. We now provide evidence that Pol-V is required for MOM1-mediated suppression of transcription at a subset of its chromosomal targets. Thus, Pol-V genetically interacts with MOM1 in the control of gene silencing. Interestingly, functional cooperation of MOM1 and Pol-V not only broadens the range of the controlled loci in comparison to each individual factor, but also determines the degree of TGS.


Asunto(s)
Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Regulación de la Expresión Génica de las Plantas , Silenciador del Gen , Proteínas Nucleares/genética , Factores de Transcripción/genética , ATPasas Asociadas con Actividades Celulares Diversas , Arabidopsis/metabolismo , Línea Celular , Metilación de ADN , ARN Polimerasas Dirigidas por ADN/genética , Elementos de Facilitación Genéticos , Epigénesis Genética , Mutación , Proteínas Nucleares/metabolismo , Regiones Promotoras Genéticas , ARN Interferente Pequeño/análisis , Factores de Transcripción/metabolismo
17.
EMBO J ; 28(1): 48-57, 2009 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-19078964

RESUMEN

We used a transgene system to study spreading of RNA-directed DNA methylation (RdDM) during transcriptional gene silencing in Arabidopsis thaliana. Forward and reverse genetics approaches using this system delineated a stepwise pathway for the biogenesis of secondary siRNAs and unidirectional spreading of methylation from an upstream enhancer element into downstream sequences. Trans-acting, hairpin-derived primary siRNAs induce primary RdDM, independently of an enhancer-associated 'nascent' RNA, at the target enhancer region. Primary RdDM is a key step in the pathway because it attracts the secondary siRNA-generating machinery, including RNA polymerase IV, RNA-dependent RNA polymerase2 and Dicer-like3 (DCL3). These factors act in a turnover pathway involving a nascent RNA, which normally accumulates stably in non-silenced plants, to produce cis-acting secondary siRNAs that induce methylation in the downstream region. The identification of DCL3 in a forward genetic screen for silencing-defective mutants demonstrated a strict requirement for 24-nt siRNAs to direct methylation. A similar stepwise process for spreading of DNA methylation may occur in mammalian genomes, which are extensively transcribed in upstream regulatory regions.


Asunto(s)
Arabidopsis/metabolismo , Arabidopsis/fisiología , Metilación de ADN , Silenciador del Gen , ARN Interferente Pequeño/metabolismo , Proteínas de Arabidopsis/metabolismo , ARN Polimerasas Dirigidas por ADN/metabolismo , Unión Proteica , ARN Polimerasa Dependiente del ARN/metabolismo , Ribonucleasa III/metabolismo
18.
PLoS Genet ; 6(10): e1001175, 2010 Oct 28.
Artículo en Inglés | MEDLINE | ID: mdl-21060865

RESUMEN

Constitutive heterochromatin comprising the centromeric and telomeric parts of chromosomes includes DNA marked by high levels of methylation associated with histones modified by repressive marks. These epigenetic modifications silence transcription and ensure stable inheritance of this inert state. Although environmental cues can alter epigenetic marks and lead to modulation of the transcription of genes located in euchromatic parts of the chromosomes, there is no evidence that external stimuli can globally destabilize silencing of constitutive heterochromatin. We have found that heterochromatin-associated silencing in Arabidopsis plants subjected to a particular temperature regime is released in a genome-wide manner. This occurs without alteration of repressive epigenetic modifications and does not involve common epigenetic mechanisms. Such induced release of silencing is mostly transient, and rapid restoration of the silent state occurs without the involvement of factors known to be required for silencing initiation. Thus, our results reveal new regulatory aspects of transcriptional repression in constitutive heterochromatin and open up possibilities to identify the molecular mechanisms involved.


Asunto(s)
Arabidopsis/genética , Heterocromatina/genética , Estrés Fisiológico , Transcripción Genética/genética , Arabidopsis/crecimiento & desarrollo , Frío , Perfilación de la Expresión Génica , Glucuronidasa/genética , Glucuronidasa/metabolismo , Histonas/metabolismo , Lisina/metabolismo , Metilación/efectos de los fármacos , Análisis de Secuencia por Matrices de Oligonucleótidos , Plantas Modificadas Genéticamente , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Plantones/genética , Plantones/crecimiento & desarrollo , Cloruro de Sodio/farmacología , Temperatura , Factores de Tiempo , Activación Transcripcional/efectos de los fármacos
19.
EMBO Rep ; 11(1): 65-71, 2010 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-20010803

RESUMEN

RNA-directed DNA methylation (RdDM) in plants requires two RNA polymerase (Pol) II-related RNA polymerases, namely Pol IV and Pol V. A genetic screen designed to reveal factors that are important for RdDM in a developmental context in Arabidopsis identified DEFECTIVE IN MERISTEM SILENCING 4 (DMS4). Unlike other mutants defective in RdDM, dms4 mutants have a pleiotropic developmental phenotype. The DMS4 protein is similar to yeast IWR1 (interacts with RNA polymerase II), a conserved putative transcription factor that interacts with Pol II subunits. The DMS4 complementary DNA partly complements the K1 killer toxin hypersensitivity of a yeast iwr1 mutant, suggesting some functional conservation. In the transgenic system studied, mutations in DMS4 directly or indirectly affect Pol IV-dependent secondary short interfering RNAs, Pol V-mediated RdDM, Pol V-dependent synthesis of intergenic non-coding RNA and expression of many Pol II-driven genes. These data suggest that DMS4 might be a regulatory factor for several RNA polymerases, thus explaining its diverse roles in the plant.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/crecimiento & desarrollo , Arabidopsis/metabolismo , Metilación de ADN/fisiología , Regulación de la Expresión Génica de las Plantas/fisiología , ARN de Planta/metabolismo , Factores de Transcripción/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Metilación de ADN/genética , ADN de Plantas/genética , ADN de Plantas/metabolismo , ARN Polimerasas Dirigidas por ADN/metabolismo , Regulación de la Expresión Génica de las Plantas/genética , Silenciador del Gen/fisiología , Mutación , Fenotipo , ARN de Planta/genética , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo , ARN no Traducido/genética , ARN no Traducido/metabolismo , Factores de Transcripción/genética
20.
Curr Opin Plant Biol ; 70: 102297, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36108411

RESUMEN

Maintaining global food security is a major challenge that requires novel strategies for crop improvement. Epigenetic regulation of plant responses to adverse environmental conditions provides a tunable mechanism to optimize plant growth, adaptation and ultimately yield. Epibreeding employs agricultural practices that rely on key epigenetic features as a means of engineering favorable phenotypic traits in target crops. This review summarizes recent findings on the role of epigenetic marks such as DNA methylation and histone modifications, in controlling phenotypic variation in crop species in response to environmental factors. The potential use of natural and induced epigenetic features as platforms for crop improvement via epibreeding, is discussed.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Metilación de ADN/genética , Productos Agrícolas/genética , Código de Histonas , Fenotipo
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