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Böhmdorfer G, Sethuraman S, Rowley MJ, Krzyszton M, Rothi MH, Bouzit L, Wierzbicki AT. Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin. eLife 2016; 5. [PMID: 27779094 PMCID: PMC5079748 DOI: 10.7554/elife.19092] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/06/2016] [Indexed: 01/10/2023] Open
Abstract
RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4. Pol V-dependent DNA methylation is established on both strands of DNA and is tightly restricted to Pol V-transcribed regions. This indicates that chromatin modifications are established in close proximity to Pol V. Finally, Pol V transcription is preferentially enriched on edges of silenced transposable elements, where Pol V transcribes into TEs. We propose that Pol V may play an important role in the determination of heterochromatin boundaries. DOI:http://dx.doi.org/10.7554/eLife.19092.001
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Affiliation(s)
- Gudrun Böhmdorfer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Shriya Sethuraman
- Bioinformatics Graduate Program, University of Michigan, Ann Arbor, United States
| | - M Jordan Rowley
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Michal Krzyszton
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - M Hafiz Rothi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Lilia Bouzit
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
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52
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Dias GB, Heringer P, Svartman M, Kuhn GCS. Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression. Chromosome Res 2016; 23:597-613. [PMID: 26408292 DOI: 10.1007/s10577-015-9480-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species. It has been assumed that CTRs have independent origins. Herein, we identify a subset of DINEs, termed DINE-TR1, which contain homologous CTRs of approximately 150 bp. We found DINE-TR1 in the sequenced genomes of several Drosophila species and in Bactrocera tryoni (Acalyptratae, Diptera). However, interspecific high sequence identity (∼ 88 %) is limited to the first ∼ 30 bp of each tandem repeat, implying that evolutionary constraints operate differently over the monomer length. DINE-TR1 is unevenly distributed across the Drosophila phylogeny. Nevertheless, sequence analysis suggests vertical transmission. We found that CTRs within DINE-TR1 have independently expanded into satellite DNA-like arrays at least twice within Drosophila. By analyzing the genome of Drosophila virilis and Drosophila americana, we show that DINE-TR1 is highly abundant in pericentromeric heterochromatin boundaries, some telomeric regions and in the Y chromosome. It is also present in the centromeric region of one autosome from D. virilis and dispersed throughout several euchromatic sites in both species. We further found that DINE-TR1 is abundant at piRNA clusters, and small DINE-TR1-derived RNA transcripts (∼25 nt) are predominantly expressed in the testes and the ovaries, suggesting active targeting by the piRNA machinery. These features suggest potential piRNA-mediated regulatory roles for DINEs at local and genome-wide scales in Drosophila.
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Affiliation(s)
- Guilherme B Dias
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro Heringer
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gustavo C S Kuhn
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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53
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Deleris A, Halter T, Navarro L. DNA Methylation and Demethylation in Plant Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:579-603. [PMID: 27491436 DOI: 10.1146/annurev-phyto-080615-100308] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Detection of plant and animal pathogens triggers a massive transcriptional reprogramming, which is directed by chromatin-based processes, and ultimately results in antimicrobial immunity. Although the implication of histone modifications in orchestrating biotic stress-induced transcriptional reprogramming has been well characterized, very little was known, until recently, about the role of DNA methylation and demethylation in this process. In this review, we summarize recent findings on the dynamics and biological relevance of DNA methylation and demethylation in plant immunity against nonviral pathogens. In particular, we report the implications of these epigenetic regulatory processes in the transcriptional and co-transcriptional control of immune-responsive genes and discuss their relevance in fine-tuning antimicrobial immune responses. Finally, we discuss the possible yet elusive role of DNA methylation and demethylation in systemic immune responses, transgenerational immune priming, and de novo epiallelism, which could be adaptive.
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Affiliation(s)
- A Deleris
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, Unité 1024, PSL Research University, 75005 Paris, France;
| | - T Halter
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, Unité 1024, PSL Research University, 75005 Paris, France;
| | - L Navarro
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, Unité 1024, PSL Research University, 75005 Paris, France;
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54
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Hirsch CD, Springer NM. Transposable element influences on gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:157-165. [PMID: 27235540 DOI: 10.1016/j.bbagrm.2016.05.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) comprise a major portion of many plant genomes and bursts of TE movements cause novel genomic variation within species. In order to maintain proper gene function, plant genomes have evolved a variety of mechanisms to tolerate the presence of TEs within or near genes. Here, we review our understanding of the interactions between TEs and gene expression in plants by assessing three ways that transposons can influence gene expression. First, there is growing evidence that TE insertions within introns or untranslated regions of genes are often tolerated and have minimal impact on expression level or splicing. However, there are examples in which TE insertions within genes can result in aberrant or novel transcripts. Second, TEs can provide novel alternative promoters, which can lead to new expression patterns or original coding potential of an alternate transcript. Third, TE insertions near genes can influence regulation of gene expression through a variety of mechanisms. For example, TEs may provide novel cis-acting regulatory sites behaving as enhancers or insert within existing enhancers to influence transcript production. Alternatively, TEs may change chromatin modifications in regions near genes, which in turn can influence gene expression levels. Together, the interactions of genes and TEs provide abundant evidence for the role of TEs in changing basic functions within plant genomes beyond acting as latent genomic elements or as simple insertional mutagens. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids. Proc Natl Acad Sci U S A 2016; 113:E2083-92. [PMID: 27001853 DOI: 10.1073/pnas.1600672113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.
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56
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A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity. Sci Rep 2016; 6:23181. [PMID: 26976262 PMCID: PMC4791638 DOI: 10.1038/srep23181] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/25/2016] [Indexed: 01/05/2023] Open
Abstract
Transposable elements (TEs), or transposons, play an important role in adaptation. TE insertion can affect host gene function and provides a mechanism for rapid increases in genetic diversity, particularly because many TEs respond to environmental stress. In the current study, we show that the transposition of a heat-activated retrotransposon, ONSEN, generated a mutation in an abscisic acid (ABA) responsive gene, resulting in an ABA-insensitive phenotype in Arabidopsis, suggesting stress tolerance. Our results provide direct evidence that a transposon activated by environmental stress could alter the genome in a potentially positive manner. Furthermore, the ABA-insensitive phenotype was inherited when the transcription was disrupted by an ONSEN insertion, whereas ABA sensitivity was recovered when the effects of ONSEN were masked by IBM2. These results suggest that epigenetic mechanisms in host plants typically buffered the effect of a new insertion, but could selectively “turn on” TEs when stressed.
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57
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Espinas NA, Saze H, Saijo Y. Epigenetic Control of Defense Signaling and Priming in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1201. [PMID: 27563304 PMCID: PMC4980392 DOI: 10.3389/fpls.2016.01201] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/28/2016] [Indexed: 05/20/2023]
Abstract
Immune recognition of pathogen-associated molecular patterns or effectors leads to defense activation at the pathogen challenged sites. This is followed by systemic defense activation at distant non-challenged sites, termed systemic acquired resistance (SAR). These inducible defenses are accompanied by extensive transcriptional reprogramming of defense-related genes. SAR is associated with priming, in which a subset of these genes is kept at a poised state to facilitate subsequent transcriptional regulation. Transgenerational inheritance of defense-related priming in plants indicates the stability of such primed states. Recent studies have revealed the importance and dynamic engagement of epigenetic mechanisms, such as DNA methylation and histone modifications that are closely linked to chromatin reconfiguration, in plant adaptation to different biotic stresses. Herein we review current knowledge regarding the biological significance and underlying mechanisms of epigenetic control for immune responses in plants. We also argue for the importance of host transposable elements as critical regulators of interactions in the evolutionary "arms race" between plants and pathogens.
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Affiliation(s)
- Nino A. Espinas
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate UniversityOkinawa, Japan
- *Correspondence: Nino A. Espinas, Yusuke Saijo,
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate UniversityOkinawa, Japan
| | - Yusuke Saijo
- Nara Institute of Science and TechnologyIkoma, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and TechnologyKawaguchi, Japan
- *Correspondence: Nino A. Espinas, Yusuke Saijo,
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58
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Zavallo D, Debat HJ, Conti G, Manacorda CA, Rodriguez MC, Asurmendi S. Differential mRNA Accumulation upon Early Arabidopsis thaliana Infection with ORMV and TMV-Cg Is Associated with Distinct Endogenous Small RNAs Level. PLoS One 2015; 10:e0134719. [PMID: 26237414 PMCID: PMC4597857 DOI: 10.1371/journal.pone.0134719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/13/2015] [Indexed: 12/04/2022] Open
Abstract
Small RNAs (sRNAs) play important roles in plant development and host-pathogen interactions. Several studies have highlighted the relationship between viral infections, endogenous sRNA accumulation and transcriptional changes associated with symptoms. However, few studies have described a global analysis of endogenous sRNAs by comparing related viruses at early stages of infection, especially before viral accumulation reaches systemic tissues. An sRNA high-throughput sequencing of Arabidopsis thaliana leaf samples infected either with Oilseed rape mosaic virus (ORMV) or crucifer-infecting Tobacco mosaic virus (TMV-Cg) with slightly different symptomatology at two early stages of infection (2 and 4dpi) was performed. At early stages, both viral infections strongly alter the patterns of several types of endogenous sRNA species in distal tissues with no virus accumulation suggesting a systemic signaling process foregoing to virus spread. A correlation between sRNAs derived from protein coding genes and the associated mRNA transcripts was also detected, indicating that an unknown recursive mechanism is involved in a regulatory circuit encompassing this sRNA/mRNA equilibrium. This work represents the initial step in uncovering how differential accumulation of endogenous sRNAs contributes to explain the massive alteration of the transcriptome associated with plant-virus interactions.
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Affiliation(s)
- Diego Zavallo
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Humberto Julio Debat
- Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), INTA, Córdoba, Argentina
| | - Gabriela Conti
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Maria Cecilia Rodriguez
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA-INTA, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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59
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To TK, Saze H, Kakutani T. DNA Methylation within Transcribed Regions. PLANT PHYSIOLOGY 2015; 168:1219-25. [PMID: 26143255 PMCID: PMC4528756 DOI: 10.1104/pp.15.00543] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 07/02/2015] [Indexed: 05/10/2023]
Abstract
DNA methylation within transcribed genes is commonly found in diverse animals and plants. Here, we provide an overview of recent advances and the remaining mystery regarding intragenic DNA methylation.
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Affiliation(s)
- Taiko K To
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan (T.K.T., T.K.); andOkinawa Institute of Science and Technology, Onna-son, Okinawa 904-0412, Japan (H.S.)
| | - Hidetoshi Saze
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan (T.K.T., T.K.); andOkinawa Institute of Science and Technology, Onna-son, Okinawa 904-0412, Japan (H.S.)
| | - Tetsuji Kakutani
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan (T.K.T., T.K.); andOkinawa Institute of Science and Technology, Onna-son, Okinawa 904-0412, Japan (H.S.)
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60
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Le TN, Miyazaki Y, Takuno S, Saze H. Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana. Nucleic Acids Res 2015; 43:3911-21. [PMID: 25813042 PMCID: PMC4417168 DOI: 10.1093/nar/gkv258] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/17/2015] [Indexed: 11/30/2022] Open
Abstract
Genomes of higher eukaryotes, including plants, contain numerous transposable elements (TEs), that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects expression of nearby genes, recent studies reveal the presence of intragenic TEs marked by repressive heterochromatic epigenetic marks within transcribed genes. However, even for the well-studied plant model Arabidopsis thaliana, the abundance of intragenic TEs, how they are epigenetically regulated, and their potential impacts on host gene expression, remain unexplored. In this study, we comprehensively analyzed genome-wide distribution and epigenetic regulation of intragenic TEs in A. thaliana. Our analysis revealed that about 3% of TEs are located within gene bodies, dominantly at intronic regions. Most of them are shorter and less methylated than intergenic TEs, but they are still targeted by RNA-directed DNA methylation-dependent and independent pathways. Surprisingly, the heterochromatic epigenetic marks at TEs are maintained within actively transcribed genes. Moreover, the heterochromatic state of intronic TEs is critical for proper transcription of associated genes. Our study provides the first insight into how intragenic TEs affect the transcriptional landscape of the A. thaliana genome, and suggests the importance of epigenetic mechanisms for regulation of TEs within transcriptional gene units.
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Affiliation(s)
- Tu N Le
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yuji Miyazaki
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Shohei Takuno
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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61
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Hunt AG. The Arabidopsis polyadenylation factor subunit CPSF30 as conceptual link between mRNA polyadenylation and cellular signaling. CURRENT OPINION IN PLANT BIOLOGY 2014; 21:128-132. [PMID: 25104048 DOI: 10.1016/j.pbi.2014.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Alternative polyadenylation plays important roles in growth processes in plants. Although the scope and significance of the phenomenon have been described to considerable extent, the mechanisms that govern differential poly(A) site selection remain active areas of investigation. Of particular interest are the means by which the factors that control differential poly(A) site choice are themselves activated and inhibited. In this review, the case is made that one particular Arabidopsis polyadenylation factor subunit, termed AtCPSF30, stands out as a conceptual link between cellular signaling pathways and differential poly(A) site choice.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA.
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62
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West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM. Genomic distribution of H3K9me2 and DNA methylation in a maize genome. PLoS One 2014; 9:e105267. [PMID: 25122127 PMCID: PMC4133378 DOI: 10.1371/journal.pone.0105267] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/18/2014] [Indexed: 11/24/2022] Open
Abstract
DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.
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Affiliation(s)
- Patrick T. West
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Qing Li
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lexiang Ji
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Steven R. Eichten
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas-Austin, Austin, Texas, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas-Austin, Austin, Texas, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Nathan M. Springer
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
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63
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Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. TRENDS IN PLANT SCIENCE 2014; 19:320-6. [PMID: 24618094 DOI: 10.1016/j.tplants.2014.01.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 05/06/2023]
Abstract
Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.
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Affiliation(s)
- M Yvonne Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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64
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Mathieu O, Bouché N. Interplay between chromatin and RNA processing. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:60-65. [PMID: 24631845 DOI: 10.1016/j.pbi.2014.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/16/2013] [Accepted: 02/12/2014] [Indexed: 06/03/2023]
Abstract
The processing of pre-mRNAs, including the selection of polyadenylation sites, is influenced by the surrounding chromatin context. We review here recent studies in Arabidopsis thaliana highlighting the intricate and reciprocal interplay between chromatin state and RNA processing. The studies have revealed that transcription can be influenced by the presence, in gene introns, of combination of epigenetic marks typical of heterochromatin. New factors binding to these marks have been identified and shown to play key roles in controlling the use of polyadenylation sites and processing of functional mRNAs. Concomitantly, several proteins of both the splicing and the polyadenylation machineries are also emerging as regulators of DNA methylation patterns and chromatin silencing.
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Affiliation(s)
- Olivier Mathieu
- Clermont Université, Université Blaise Pascal, GReD, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6293, GReD, F-63001 Clermont-Ferrand, France; INSERM, UMR 1103, GReD, F-63001 Clermont-Ferrand, France.
| | - Nicolas Bouché
- INRA, UMR 1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France.
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65
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Rataj K, Simpson GG. Message ends: RNA 3' processing and flowering time control. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:353-63. [PMID: 24363425 DOI: 10.1093/jxb/ert439] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plants control the time at which they flower in order to ensure reproductive success. This control is underpinned by precision in gene regulation acting through genetically separable pathways. The genetic dissection of this process in the model plant Arabidopsis thaliana has led to the recurrent identification of plant-specific and highly conserved RNA 3' end processing factors required to control flowering by specifically controlling transcription of mRNA encoding the floral repressor FLOWERING LOCUS C (FLC). Here, we review the features of these RNA-processing and RNA-associated proteins, and the complex architecture of coding and non-coding RNA transcription at the FLC locus. We discuss alternative concepts that might explain how these RNA-processing events regulate FLC transcription and hence control flowering time.
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Affiliation(s)
- Katarzyna Rataj
- College of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
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Coustham V, Vlad D, Deremetz A, Gy I, Cubillos FA, Kerdaffrec E, Loudet O, Bouché N. SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1. PLoS One 2014; 9:e84687. [PMID: 24404182 PMCID: PMC3880313 DOI: 10.1371/journal.pone.0084687] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/26/2013] [Indexed: 11/17/2022] Open
Abstract
Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.
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Affiliation(s)
- Vincent Coustham
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Daniela Vlad
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Aurélie Deremetz
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Isabelle Gy
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Francisco A Cubillos
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Envel Kerdaffrec
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Olivier Loudet
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
| | - Nicolas Bouché
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, Versailles, France ; AgroParisTech, Institut Jean-Pierre Bourgin, RD10, Versailles, France
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Khan AR, Enjalbert J, Marsollier AC, Rousselet A, Goldringer I, Vitte C. Vernalization treatment induces site-specific DNA hypermethylation at the VERNALIZATION-A1 (VRN-A1) locus in hexaploid winter wheat. BMC PLANT BIOLOGY 2013; 13:209. [PMID: 24330651 PMCID: PMC3890506 DOI: 10.1186/1471-2229-13-209] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/25/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND Certain temperate species require prolonged exposure to low temperature to initiate transition from vegetative growth to flowering, a process known as vernalization. In wheat, winter cultivars require vernalization to initiate flowering, making vernalization requirement a trait of key importance in wheat agronomy. The genetic bases of vernalization response have been largely studied in wheat, leading to the characterization of a regulation pathway that involves the key gene VERNALIZATION1 (VRN1). While previous studies in wheat and barley have revealed the functional role of histone modification in setting VRN1 expression, other mechanisms might also be involved. Here, we were interested in determining whether the cold-induced expression of the wheat VRN-A1 gene is associated with a change in DNA methylation. RESULTS We provide the first DNA methylation analysis of the VRN-A1 gene, and describe the existence of methylation at CG but also at non CG sites. While CG sites show a bell-shape profile typical of gene-body methylation, non CG methylation is restricted to the large (8.5 kb) intron 1, in a region harboring fragments of transposable elements (TEs). Interestingly, cold induces a site-specific hypermethylation at these non CG sites. This increase in DNA methylation is transmitted through mitosis, and is reset to its original level after sexual reproduction. CONCLUSIONS These results demonstrate that VRN-A1 has a particular DNA methylation pattern, exhibiting rapid shift within the life cycle of a winter wheat plant following exposure to particular environmental conditions. The finding that this shift occurs at non CG sites in a TE-rich region opens interesting questions onto the possible consequences of this type of methylation in gene expression.
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Affiliation(s)
| | | | | | - Agnès Rousselet
- INRA, UMR de Génétique Végétale, Gif sur Yvette F-91190, France
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Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc Natl Acad Sci U S A 2013; 111:527-32. [PMID: 24248388 DOI: 10.1073/pnas.1320106110] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is important for the silencing of transposons and other repetitive elements in many higher eukaryotes. However, plant and mammalian genomes have evolved to contain repetitive elements near or inside their genes. How these genes are kept from being silenced by DNA methylation is not well understood. A forward genetics screen led to the identification of the putative chromatin regulator Enhanced Downy Mildew 2 (EDM2) as a cellular antisilencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite Plant Homeo Domain that recognizes both active and repressive histone methylation marks at the intronic repeat elements in genes such as the Histone 3 lysine 9 demethylase gene Increase in BONSAI Methylation 1 (IBM1) and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes. Our results thus increase the understanding of antisilencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.
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