1
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Li S, Yan J, Chen LG, Meng G, Zhou Y, Wang CM, Jiang L, Luo J, Jiang Y, Li QF, Tang W, He JX. Brassinosteroid regulates stomatal development in etiolated Arabidopsis cotyledons via transcription factors BZR1 and BES1. PLANT PHYSIOLOGY 2024; 195:1382-1400. [PMID: 38345866 DOI: 10.1093/plphys/kiae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 12/19/2023] [Indexed: 06/02/2024]
Abstract
Brassinosteroids (BRs) are phytohormones that regulate stomatal development. In this study, we report that BR represses stomatal development in etiolated Arabidopsis (Arabidopsis thaliana) cotyledons via transcription factors BRASSINAZOLE RESISTANT 1 (BZR1) and bri1-EMS SUPPRESSOR1 (BES1), which directly target MITOGEN-ACTIVATED PROTEIN KINASE KINASE 9 (MKK9) and FAMA, 2 important genes for stomatal development. BZR1/BES1 bind MKK9 and FAMA promoters in vitro and in vivo, and mutation of the BZR1/BES1 binding motif in MKK9/FAMA promoters abolishes their transcription regulation by BZR1/BES1 in plants. Expression of a constitutively active MKK9 (MKK9DD) suppressed overproduction of stomata induced by BR deficiency, while expression of a constitutively inactive MKK9 (MKK9KR) induced high-density stomata in bzr1-1D. In addition, bzr-h, a sextuple mutant of the BZR1 family of proteins, produced overabundant stomata, and the dominant bzr1-1D and bes1-D mutants effectively suppressed the stomata-overproducing phenotype of brassinosteroid insensitive 1-116 (bri1-116) and brassinosteroid insensitive 2-1 (bin2-1). In conclusion, our results revealed important roles of BZR1/BES1 in stomatal development, and their transcriptional regulation of MKK9 and FAMA expression may contribute to BR-regulated stomatal development in etiolated Arabidopsis cotyledons.
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Affiliation(s)
- Shuo Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaptation Biology, School of Life Sciences, Shandong University, Qingdao 266237, Shandong, China
| | - Jin Yan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, China
| | - Lian-Ge Chen
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, China
| | - Guanghua Meng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
| | - Yuling Zhou
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
| | - Chun-Ming Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
| | - Lei Jiang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
| | - Juan Luo
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Qian-Feng Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, China
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR 00000, China
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2
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Kenchanmane Raju SK, Lensink M, Kliebenstein DJ, Niederhuth C, Monroe G. Epigenomic divergence correlates with sequence polymorphism in Arabidopsis paralogs. THE NEW PHYTOLOGIST 2023; 240:1292-1304. [PMID: 37614211 DOI: 10.1111/nph.19227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/26/2023] [Indexed: 08/25/2023]
Abstract
Processes affecting rates of sequence polymorphism are fundamental to the evolution of gene duplicates. The relationship between gene activity and sequence polymorphism can influence the likelihood that functionally redundant gene copies are co-maintained in stable evolutionary equilibria vs other outcomes such as neofunctionalization. Here, we investigate genic variation in epigenome-associated polymorphism rates in Arabidopsis thaliana and consider whether these affect the evolution of gene duplicates. We compared the frequency of sequence polymorphism and patterns of genetic differentiation between genes classified by exon methylation patterns: unmethylated (unM), gene-body methylated (gbM), and transposon-like methylated (teM) states, which reflect divergence in gene expression. We found that the frequency of polymorphism was higher in teM (transcriptionally repressed, tissue-specific) genes and lower in gbM (active, constitutively expressed) genes. Comparisons of gene duplicates were largely consistent with genome-wide patterns - gene copies that exhibit teM accumulate more variation, evolve faster, and are in chromatin states associated with reduced DNA repair. This relationship between expression, the epigenome, and polymorphism may lead to the breakdown of equilibrium states that would otherwise maintain genetic redundancies. Epigenome-mediated polymorphism rate variation may facilitate the evolution of novel gene functions in duplicate paralogs maintained over evolutionary time.
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Affiliation(s)
| | - Mariele Lensink
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
| | - Grey Monroe
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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3
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Kim JH, Jung WJ, Kim MS, Seo YW. The wheat TaF-box3, SCF ubiquitin ligase component, participates in the regulation of flowering time in transgenic Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111668. [PMID: 36858206 DOI: 10.1016/j.plantsci.2023.111668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Histone methylation is actively involved in plant flowering time and is regulated by a myriad of genetic pathways that integrate endogenous and exogenous signals. We identified an F-box gene from wheat (Triticum aestivum L.) and named it TaF-box3. Transcript expression analysis showed that TaF-box3 expression was gradually induced during the floret development and anthesis stages (WS2.5-10). Furthermore, ubiquitination assays have shown that TaF-box3 is a key component of the SCF ubiquitin ligase complex. TaF-box3 overexpression in Arabidopsis resulted in an early flowering phenotype and different cell sizes in leaves compared to the WT. Furthermore, the transcript level of a flowering time-related gene was significantly reduced in TaF-box3 overexpressing plants, which was linked with lower histone H3 Lys4 trimethylation (H3K4me3) and H3 Lys36 trimethylation (H3K36me3). Overexpression of TaF-box3 in Arabidopsis was shown to be involved in the regulation of flowering time by demethylating FLC chromatin, according to ChIP experiments. Protein analysis confirmed that TaMETS interacts with TaF-box3 and is ubiquitinated and degraded in a TaF-box3-dependnent manner. Based on these findings, we propose that TaF-box3 has a positive role in flowering time, which leads to a better understanding of TaF-box3 physiological mechanism in Arabidopsis.
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Affiliation(s)
- Jae Ho Kim
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea; Institute of Animal Molecular Biotechnology, Korea University, Seoul, the Republic of Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul, the Republic of Korea
| | - Moon Seok Kim
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, the Republic of Korea; Ojeong Plant Breeding Research Center, Korea University, Seoul, the Republic of Korea.
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4
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Zhou D, Wang X, Wang X, Mao T. PHYTOCHROME INTERACTING FACTOR 4 regulates microtubule organization to mediate high temperature-induced hypocotyl elongation in Arabidopsis. THE PLANT CELL 2023; 35:2044-2061. [PMID: 36781395 PMCID: PMC10226600 DOI: 10.1093/plcell/koad042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 05/30/2023]
Abstract
Hypocotyl elongation is an important morphological response during plant thermomorphogenesis. Multiple studies indicate that the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) is a key regulator of high temperature-induced hypocotyl elongation. However, the underlying cellular mechanisms regarding PIF4-mediated hypocotyl elongation are largely unclear. In this study, we found that PIF4 regulates the PLANT U-BOX TYPE E3 UBIQUITIN LIGASE 31 (PUB31)-SPIRAL1 (SPR1) module and alters cortical microtubule reorganization to promote hypocotyl cell elongation during Arabidopsis thaliana (Arabidopsis) thermomorphogenesis. SPR1 loss-of-function mutants exhibit much shorter hypocotyls when grown at 28 °C, indicating a positive role for SPR1 in high ambient temperature-induced hypocotyl elongation. High ambient temperature induces SPR1 expression in a PIF4-dependent manner, and stabilizes SPR1 protein to mediate microtubule reorganization. Further investigation showed that PUB31 interacts with and ubiquitinates SPR1. In particular, the ubiquitinated effect on SPR1 was moderately decreased at high temperature, which was due to the direct binding of PIF4 to the PUB31 promoter and down-regulating its expression. Thus, this study reveals a mechanism in which PIF4 induces SPR1 expression and suppresses PUB31 expression, resulting in the accumulation and stabilization of SPR1 protein, and further promoting hypocotyl cell elongation by altering cortical microtubule organization during Arabidopsis thermomorphogenesis.
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Affiliation(s)
- Dingding Zhou
- State Key Laboratory of Plant Environmental Resilience, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohong Wang
- State Key Laboratory of Plant Environmental Resilience, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangfeng Wang
- State Key Laboratory of Plant Environmental Resilience, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tonglin Mao
- State Key Laboratory of Plant Environmental Resilience, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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5
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Jiang Y, Zhang S, Chen K, Xia X, Tao B, Kong W. Impacts of DNA methylases and demethylases on the methylation and expression of Arabidopsis ethylene signal pathway genes. Funct Integr Genomics 2023; 23:143. [PMID: 37127698 DOI: 10.1007/s10142-023-01069-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
Arabidopsis ethylene (ET) signal pathway plays important roles in various aspects. Cytosine DNA methylation is significant in controlling gene expression in plants. Here, we analyzed the bisulfite sequencing and mRNA sequencing data from Arabidopsis (de)methylase mutants met1, cmt3, drm1/2, ddm1, ros1-4, and rdd to investigate how DNA (de)methylases influence the DNA methylation and expression of Arabidopsis ET pathway genes. At least 32 genes are found to involved in Arabidopsis ET pathway by text mining. Among them, 14 genes are unmethylated or methylated with very low levels. ACS6 and ACS9 are conspicuously methylated within their upstream regions. The other 16 genes are predominantly methylated at the CG sites within gene body regions in wild-type plants, and mutation of MET1 resulted in almost entire elimination of the CG methylations. In addition, CG methylations within some genes are jointly maintained by MET1 and other (de)methylases. Analyses of mRNA-seq data indicated that some ET pathway genes were differentially expressed between wild-type and diverse mutants. PDF1.2, the marker gene of ET signal pathway, was found being regulated indirectly by the methylases. Eighty-two transposable elements (TEs) were identified to be associated to 15 ET pathway genes. ACS11 is found located in a heterochromatin region that contains 57 TEs, indicating its specific expression and regulation. Together, our results suggest that DNA (de)methylases are implicated in the regulation of CG methylation within gene body regions and transcriptional activity of some ET pathway genes and that maintenance of normal CG methylation is essential for ET pathway in Arabidopsis.
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Affiliation(s)
- Yan Jiang
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shengwei Zhang
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Kun Chen
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xue Xia
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Bingqing Tao
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Weiwen Kong
- School of Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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6
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Manh MB, Ost C, Peiter E, Hause B, Krupinska K, Humbeck K. WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications. Int J Mol Sci 2023; 24:ijms24076326. [PMID: 37047301 PMCID: PMC10094662 DOI: 10.3390/ijms24076326] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.
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Affiliation(s)
- Minh Bui Manh
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University (CAU), 24098 Kiel, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
- Correspondence:
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7
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Radjacommare R, Lin SY, Usharani R, Lin WD, Jauh GY, Schmidt W, Fu H. The Arabidopsis Deubiquitylase OTU5 Suppresses Flowering by Histone Modification-Mediated Activation of the Major Flowering Repressors FLC, MAF4, and MAF5. Int J Mol Sci 2023; 24:ijms24076176. [PMID: 37047144 PMCID: PMC10093928 DOI: 10.3390/ijms24076176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Distinct phylogeny and substrate specificities suggest that 12 Arabidopsis Ovarian Tumor domain-containing (OTU) deubiquitinases participate in conserved or plant-specific functions. The otu5-1 null mutant displayed a pleiotropic phenotype, including early flowering, mimicking that of mutants harboring defects in subunits (e.g., ARP6) of the SWR1 complex (SWR1c) involved in histone H2A.Z deposition. Transcriptome and RT-qPCR analyses suggest that downregulated FLC and MAF4-5 are responsible for the early flowering of otu5-1. qChIP analyses revealed a reduction and increase in activating and repressive histone marks, respectively, on FLC and MAF4-5 in otu5-1. Subcellular fractionation, GFP-fusion expression, and MNase treatment of chromatin showed that OTU5 is nucleus-enriched and chromatin-associated. Moreover, OTU5 was found to be associated with FLC and MAF4-5. The OTU5-associated protein complex(es) appears to be distinct from SWR1c, as the molecular weights of OTU5 complex(es) were unaltered in arp6-1 plants. Furthermore, the otu5-1 arp6-1 double mutant exhibited synergistic phenotypes, and H2A.Z levels on FLC/MAF4-5 were reduced in arp6-1 but not otu5-1. Our results support the proposition that Arabidopsis OTU5, acting independently of SWR1c, suppresses flowering by activating FLC and MAF4-5 through histone modification. Double-mutant analyses also indicate that OTU5 acts independently of the HUB1-mediated pathway, but it is partially required for FLC-mediated flowering suppression in autonomous pathway mutants and FRIGIDA-Col.
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8
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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9
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Vaquero-Sedas MI, Vega-Palas MA. Epigenetic nature of Arabidopsis thaliana telomeres. PLANT PHYSIOLOGY 2023; 191:47-55. [PMID: 36218957 PMCID: PMC9806604 DOI: 10.1093/plphys/kiac471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/22/2022] [Indexed: 05/15/2023]
Abstract
The epigenetic features of defined chromosomal domains condition their biochemical and functional properties. Therefore, there is considerable interest in studying the epigenetic marks present at relevant chromosomal loci. Telomeric regions, which include telomeres and subtelomeres, have been traditionally considered heterochromatic. However, whereas the heterochromatic nature of subtelomeres has been widely accepted, the epigenetic status of telomeres remains controversial. Here, we studied the epigenetic features of Arabidopsis (Arabidopsis thaliana) telomeres by analyzing multiple genome-wide ChIP-seq experiments. Our analyses revealed that Arabidopsis telomeres are not significantly enriched either in euchromatic marks like H3K4me2, H3K9ac, and H3K27me3 or in heterochromatic marks such as H3K27me1 and H3K9me2. Thus, telomeric regions in Arabidopsis have a bimodal chromatin organization with telomeres lacking significant levels of canonical euchromatic and heterochromatic marks followed by heterochromatic subtelomeres. Since heterochromatin is known to influence telomere function, the heterochromatic modifications present at Arabidopsis subtelomeres could play a relevant role in telomere biology.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville E41092, Spain
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10
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Xu F, Tang J, Wang S, Cheng X, Wang H, Ou S, Gao S, Li B, Qian Y, Gao C, Chu C. Antagonistic control of seed dormancy in rice by two bHLH transcription factors. Nat Genet 2022; 54:1972-1982. [PMID: 36471073 DOI: 10.1038/s41588-022-01240-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022]
Abstract
Preharvest sprouting (PHS) due to lack of seed dormancy seriously threatens crop production worldwide. As a complex quantitative trait, breeding of crop cultivars with suitable seed dormancy is hindered by limited useful regulatory genes. Here by repeatable phenotypic characterization of fixed recombinant individuals, we report a quantitative genetic locus, Seed Dormancy 6 (SD6), from aus-type rice, encoding a basic helix-loop-helix (bHLH) transcription factor, which underlies the natural variation of seed dormancy. SD6 and another bHLH factor inducer of C-repeat binding factors expression 2 (ICE2) function antagonistically in controlling seed dormancy by directly regulating the ABA catabolism gene ABA8OX3, and indirectly regulating the ABA biosynthesis gene NCED2 via OsbHLH048, in a temperature-dependent manner. The weak-dormancy allele of SD6 is common in cultivated rice but undergoes negative selection in wild rice. Notably, by genome editing SD6 and its wheat homologs, we demonstrated that SD6 is a useful breeding target for alleviating PHS in cereals under field conditions.
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Affiliation(s)
- Fan Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing, China
| | - Jiuyou Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shengxing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xi Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Biotechnology and Crop Quality Improvement, Ministry of Agriculture/Biotechnology Research Center, Southwest University, Chongqing, China
| | - Hongru Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Shaopei Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, China.
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11
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Wang L, Zhou F, Liu X, Zhang H, Yan T, Sun Y, Shi K, Zheng X, Zhu Y, Shan D, Bai Y, Guo Y, Kong J. ELONGATED HYPOCOTYL 5-mediated suppression of melatonin biosynthesis is alleviated by darkness and promotes cotyledon opening. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4941-4953. [PMID: 35580847 DOI: 10.1093/jxb/erac176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) biosynthesis in plants is induced by darkness and high-intensity light; however, the underlying transcriptional mechanisms and upstream signalling pathways are unknown. We identified a dark-induced and highly expressed melatonin synthetase in Arabidopsis thaliana, AtSNAT6, encoding serotonin N-acetyltransferase. We assessed melatonin content and AtSNAT6 expression in mutants lacking key regulators of light/dark signalling. AtCOP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) and AtHY5 (ELONGATED HYPOCOTYL 5), which control light/dark transition and photomorphogenesis, promoted and suppressed melatonin biosynthesis, respectively. Using EMSA and ChIP-qPCR analysis, we showed that AtHY5 inhibits AtSNAT6 expression directly. An analysis of melatonin content in snat6 hy5 double mutant and AtHY5+AtSNAT6-overexpressing plants confirmed the regulatory function of AtHY5 and AtSNAT6 in melatonin biosynthesis. Exogenous melatonin further inhibited cotyledon opening in hy5 mutant and AtSNAT6-overexpressing seedlings, but partially reversed the promotion of cotyledon opening in AtHY5-overexpressing seedlings and snat6. Additionally, CRISPR/Cas9-mediated mutation of AtSNAT6 increased cotyledon opening in hy5 mutant, and overexpression of AtSNAT6 decreased cotyledon opening in AtHY5-overexpressing seedlings via changing melatonin biosynthesis, confirming that AtHY5 decreased melatonin-mediated inhibition of cotyledon opening. Our data provide new insights into the regulation of melatonin biosynthesis and its function in cotyledon opening.
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Affiliation(s)
- Lin Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fangfang Zhou
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuan Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Haixia Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Tianci Yan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, Beijing, China
| | - Kun Shi
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaodong Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yunpeng Zhu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Dongqian Shan
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yixue Bai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yan Guo
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jin Kong
- College of Horticulture, China Agricultural University, Beijing, China
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12
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To TK, Kakutani T. Crosstalk among pathways to generate DNA methylome. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102248. [PMID: 35724481 DOI: 10.1016/j.pbi.2022.102248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Cytosine is methylated in both CpG and non-CpG contexts (mCG and mCH, respectively) in plant genomes. Although mCG and mCH are almost independent in regard to their "maintenance," recent studies uncovered crosstalk between them during their "establishment," which unexpectedly functions in both RNAi-dependent and -independent pathways. In addition, the importance of linker histone H1 and variants of histone H2A to DNA methylation dynamics is starting to be understood. We summarize these new aspects of mechanisms to generate DNA methylomes and discuss future prospects.
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Affiliation(s)
- Taiko Kim To
- Department of Biological Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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13
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Huang X, Sun MX. H3K27 methylation regulates the fate of two cell lineages in male gametophytes. THE PLANT CELL 2022; 34:2989-3005. [PMID: 35543471 PMCID: PMC9338816 DOI: 10.1093/plcell/koac136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/03/2022] [Indexed: 05/14/2023]
Abstract
During angiosperm male gametogenesis, microspores divide to produce a vegetative cell (VC) and a male germline (MG), each with distinct cell fates. The mechanism underlying determination of the MG cell/VC fate remains an important area of research, with many unanswered questions. Here, we report that H3K27me3 is essential for VC fate commitment in male Arabidopsis thaliana gametophytes; H3K27me3 erasure contributes to MG cell fate initiation. VC-targeted H3K27me3 erasure disturbed VC development and shifted the VC fate toward a gamete destination, which suggests that MG cells require H3K27me3 erasure to trigger gamete cell fate. Multi-omics and cytological analyses confirmed the occurrence of extensive cell identity transition due to H3K27me3 erasure. Therefore, we experimentally confirmed that MG cell/VC fate is epigenetically regulated. H3K27 methylation plays a critical role in guiding MG cell/VC fate determination for pollen fertility in Arabidopsis. Our work also provides evidence for two previous hypotheses: the germline cell fate is specified by the differential distribution of unknown determinants and VC maintains the default microspore program (i.e. the H3K27me3 setting) while MG requires reprogramming.
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Affiliation(s)
- Xiaorong Huang
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
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14
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Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis. Nat Commun 2022; 13:861. [PMID: 35165291 PMCID: PMC8844080 DOI: 10.1038/s41467-022-28468-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are robustly silenced by multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here, we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, though the resulting mCH/H3K9me is removed thereafter. Unexpectedly, targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG within the genome, suggesting underlying global negative controls. We propose that local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced DNA methylome patterning. In plant genomes, both mCG and H3K9me2/mCH are important for silencing transposable elements (TEs). Here, the authors show that establishment of mCH is abolished in both TE and active genes when mCG is lost and targeting efficiency of mCH depends on relative levels of mCG within the genome.
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15
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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:2115570119. [PMID: 35027454 PMCID: PMC8784105 DOI: 10.1073/pnas.2115570119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the tissue-specific defects correlate with residual ATXR6 expression. We also determined that ATXR5/6 function is essential for female germline development. Furthermore, we provide a comprehensive analysis of H3K27me1 changes in relation to other epigenetic marks. We also determined that some previously reported suppressors of atxr5/6 may act by restoring the levels of H3K27me1, such as through up-regulation of the ATXR6 transcript in the atxr6 hypomorphic promoter allele. ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6-null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.
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16
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Gao S, Zeng X, Wang J, Xu Y, Yu C, Huang Y, Wang F, Wu K, Yang S. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering. Cells 2021; 10:cells10113001. [PMID: 34831226 PMCID: PMC8616286 DOI: 10.3390/cells10113001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/31/2021] [Indexed: 01/12/2023] Open
Abstract
The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.
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Affiliation(s)
- Sujuan Gao
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Ministry of Agriculture, Guangzhou 510225, China;
| | - Xueqin Zeng
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510000, China;
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Chunwei Yu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Yishui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Feng Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
- Correspondence: (K.W.); (S.Y.)
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (K.W.); (S.Y.)
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17
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Abstract
Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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Affiliation(s)
- James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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18
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Barrero-Gil J, Mouriz A, Piqueras R, Salinas J, Jarillo JA, Piñeiro M. A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition. PLANT PHYSIOLOGY 2021; 187:462-471. [PMID: 34618146 PMCID: PMC8418395 DOI: 10.1093/plphys/kiab275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Plants react to environmental challenges by integrating external cues with endogenous signals to optimize survival and reproductive success. However, the mechanisms underlying this integration remain obscure. While stress conditions are known to impact plant development, how developmental transitions influence responses to adverse conditions has not been addressed. Here, we reveal a molecular mechanism of stress response attenuation during the onset of flowering in Arabidopsis (Arabidopsis thaliana). We show that Arabidopsis MORF-RELATED GENE (MRG) proteins, components of the NuA4 histone acetyltransferase complex that bind trimethylated-lysine 36 in histone H3 (H3K36me3), function as a chromatin switch on the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) to coordinate flowering initiation with plant responsiveness to hostile environments. MRG proteins are required to activate SOC1 expression during flowering induction by promoting histone H4 acetylation. In turn, SOC1 represses a broad array of genes that mediate abiotic stress responses. We propose that during the transition from vegetative to reproductive growth, the MRG-SOC1 module constitutes a central hub in a mechanism that tunes down stress responses to enhance the reproductive success and plant fitness at the expense of costly efforts for adaptation to challenging environments.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Raquel Piqueras
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - José A. Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
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19
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Chai M, Queralta Castillo I, Sonntag A, Wang S, Zhao Z, Liu W, Du J, Xie H, Liao F, Yun J, Jiang Q, Sun J, Molina I, Wang ZY. A seed coat-specific β-ketoacyl-CoA synthase, KCS12, is critical for preserving seed physical dormancy. PLANT PHYSIOLOGY 2021; 186:1606-1615. [PMID: 33779764 PMCID: PMC8260136 DOI: 10.1093/plphys/kiab152] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/08/2021] [Indexed: 05/21/2023]
Abstract
Physical dormancy in seeds exists widely in seed plants and plays a vital role in maintaining natural seed banks. The outermost cuticle of the seed coat forms a water-impermeable layer, which is critical for establishing seed physical dormancy. We previously set up the legume plant Medicago truncatula as an excellent model for studying seed physical dormancy, and our studies revealed that a class II KNOTTED-like homeobox, KNOX4, is a transcription factor critical for controlling hardseededness. Here we report the function of a seed coat β-ketoacyl-CoA synthase, KCS12. The expression level of KCS12 is significantly downregulated in the knox4 mutant. The KCS12 gene is predominantly expressed in the seed coat, and seed development in the M. truncatula kcs12 mutant is altered. Further investigation demonstrated that kcs12 mutant seeds lost physical dormancy and were able to absorb water without scarification treatment. Chemical analysis revealed that concentrations of C24:0 lipid polyester monomers are significantly decreased in mutant seeds, indicating that KCS12 is an enzyme that controls the production of very long chain lipid species in the seed coat. A chromatin immunoprecipitation assay demonstrated that the expression of KCS12 in the seed coat is directly regulated by the KNOX4 transcription factor. These findings define a molecular mechanism by which KNOX4 and KCS12 control formation of the seed coat and seed physical dormancy.
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Affiliation(s)
- Maofeng Chai
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Noble Research Institute, Ardmore, OK 73401, USA
| | | | - Annika Sonntag
- Department of Biology, Algoma University, Sault Ste. Marie, ON, Canada, P6A 2G4
| | - Shixing Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhili Zhao
- Noble Research Institute, Ardmore, OK 73401, USA
| | - Wei Liu
- Noble Research Institute, Ardmore, OK 73401, USA
| | - Juan Du
- Noble Research Institute, Ardmore, OK 73401, USA
| | - Hongli Xie
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Fuqi Liao
- Noble Research Institute, Ardmore, OK 73401, USA
| | - Jianfei Yun
- Noble Research Institute, Ardmore, OK 73401, USA
| | | | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Isabel Molina
- Department of Biology, Algoma University, Sault Ste. Marie, ON, Canada, P6A 2G4
| | - Zeng-Yu Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Noble Research Institute, Ardmore, OK 73401, USA
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20
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Rougée M, Quadrana L, Zervudacki J, Hure V, Colot V, Navarro L, Deleris A. Polycomb mutant partially suppresses DNA hypomethylation-associated phenotypes in Arabidopsis. Life Sci Alliance 2020; 4:4/2/e202000848. [PMID: 33443101 PMCID: PMC7756957 DOI: 10.26508/lsa.202000848] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
A mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations. In plants and mammals, DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the polycomb repressive complex 2, are considered as two specialized systems for the epigenetic silencing of transposable element (TE) and genes, respectively. Nevertheless, many TE sequences acquire H3K27me3 when DNA methylation is lost. Here, we show in Arabidopsis thaliana that the gain of H3K27me3 observed at hundreds of TEs in the ddm1 mutant defective in the maintenance of DNA methylation, essentially depends on CURLY LEAF (CLF), one of two partially redundant H3K27 methyltransferases active in vegetative tissues. Surprisingly, the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, ddm1 clf plants exhibited less activated TEs, and a chromatin recompaction as well as hypermethylation of linker DNA compared with ddm1. Thus, a mutation in polycomb repressive complex 2 does not aggravate the molecular phenotypes linked to ddm1 but instead partially suppresses them, challenging our assumptions of the relationship between two conserved epigenetic silencing pathways.
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Affiliation(s)
- Martin Rougée
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Jérôme Zervudacki
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Valentin Hure
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Lionel Navarro
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Angélique Deleris
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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21
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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22
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To TK, Nishizawa Y, Inagaki S, Tarutani Y, Tominaga S, Toyoda A, Fujiyama A, Berger F, Kakutani T. RNA interference-independent reprogramming of DNA methylation in Arabidopsis. NATURE PLANTS 2020; 6:1455-1467. [PMID: 33257860 DOI: 10.1038/s41477-020-00810-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is important for silencing transposable elements (TEs) in diverse eukaryotes, including plants. In plant genomes, TEs are silenced by methylation of histone H3 lysine 9 (H3K9) and cytosines in both CG and non-CG contexts. The role of RNA interference (RNAi) in establishing TE-specific silent marks has been extensively studied, but the importance of RNAi-independent pathways remains largely unexplored. Here, we directly investigated transgenerational de novo DNA methylation of TEs after the loss of silent marks. Our analyses uncovered potent and precise RNAi-independent pathways for recovering non-CG methylation and H3K9 methylation in most TE genes (that is, coding regions within TEs). Characterization of a subset of TE genes without the recovery revealed the effects of H3K9 demethylation, replacement of histone H2A variants and their interaction with CG methylation, together with feedback from transcription. These chromatin components are conserved among eukaryotes and may contribute to chromatin reprogramming in a conserved manner.
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Affiliation(s)
- Taiko Kim To
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuichiro Nishizawa
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Soichi Inagaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan
- PREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yoshiaki Tarutani
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan
| | - Sayaka Tominaga
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Toyoda
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Tetsuji Kakutani
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.
- Department of Integrated Genetics, National Institute of Genetics (NIG), Mishima, Shizuoka, Japan.
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Genome-Wide Identification of Epigenetic Regulators in Quercus suber L. Int J Mol Sci 2020; 21:ijms21113783. [PMID: 32471127 PMCID: PMC7313042 DOI: 10.3390/ijms21113783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.
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24
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Dalakouras A, Papadopoulou KK. Epigenetic Modifications: An Unexplored Facet of Exogenous RNA Application in Plants. PLANTS 2020; 9:plants9060673. [PMID: 32466487 PMCID: PMC7356522 DOI: 10.3390/plants9060673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 01/09/2023]
Abstract
Exogenous RNA interference (exo-RNAi) is a powerful transgene-free tool in modern crop improvement and protection platforms. In exo-RNAi approaches, double-stranded RNAs (dsRNAs) or short-interfering RNAs (siRNAs) are externally applied in plants in order to selectively trigger degradation of target mRNAs. Yet, the applied dsRNAs may also trigger unintended epigenetic alterations and result in epigenetically modified plants, an issue that has not been sufficiently addressed and which merits more careful consideration.
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Affiliation(s)
- Athanasios Dalakouras
- Department of Biochemistry & Biotechnology, University of Thessaly, 41500 Larissa, Greece;
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER, 57001 Thessaloniki, Greece
- Correspondence:
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25
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Kong W, Xia X, Wang Q, Liu LW, Zhang S, Ding L, Liu A, La H. Impact of DNA Demethylases on the DNA Methylation and Transcription of Arabidopsis NLR Genes. Front Genet 2020; 11:460. [PMID: 32528522 PMCID: PMC7264425 DOI: 10.3389/fgene.2020.00460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
Active DNA demethylation is an important epigenetic process that plays a key role in maintaining normal gene expression. In plants, active DNA demethylation is mediated by DNA demethylases, including ROS1, DME, DML2, and DML3. In this study, the available bisulfite sequencing and mRNA sequencing data from ros1 and rdd mutants were analyzed to reveal how the active DNA demethylation process shapes the DNA methylation patterns of Arabidopsis nucleotide-binding leucine-rich repeat (NLR) genes, a class of important plant disease resistance genes. We demonstrate that the CG methylation levels of three NLR genes (AT5G49140, AT5G35450, and AT5G36930) are increased in the ros1 mutants relative to the wild-type plants, whereas the CG methylation level of AT2G17050 is decreased. We also observed increased CG methylation levels of AT4G11170 and AT5G47260 and decreased CG methylation levels of AT5G38350 in rdd mutants. We further found that the expression of three NLR genes (AT1G12280, AT1G61180, and AT4G19520) was activated in both ros1 and rdd mutants, whereas the expression of another three NLR genes (AT1G58602, AT1G59620, and AT1G62630) was repressed in these two mutants. Quantitative reverse transcriptase–polymerase chain reaction detection showed that the expression levels of AT1G58602.1, AT4G19520.3, AT4G19520.4, and AT4G19520.5 were decreased in the ros1 mutant; AT3G50950.1 and AT3G50950.2 in the rdd mutant were also decreased in expression compared to Col-0, whereas AT1G57630.1, AT1G58602.2, and AT5G45510.1 were upregulated in the rdd mutant relative to Col-0. These results indicate that some NLR genes are regulated by DNA demethylases. Our study demonstrates that each DNA demethylase (ROS1, DML2, and DML3) exerts a specific effect on the DNA methylation of the NLR genes, and active DNA demethylation is part of the regulation of DNA methylation and transcriptional activity of some Arabidopsis NLR genes.
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Affiliation(s)
- Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xue Xia
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Li-Wei Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shengwei Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li Ding
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Aixin Liu
- Department of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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26
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Li H, Xue X, Li Z, Pan B, Hao Y, Niu Q. Aluminium-induced synaptic plasticity injury via the PHF8-H3K9me2-BDNF signalling pathway. CHEMOSPHERE 2020; 244:125445. [PMID: 31835052 DOI: 10.1016/j.chemosphere.2019.125445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
Aluminium is an environmental neurotoxin that comes extensively in contact with human being. The molecular mechanism of aluminium toxicity remains unclear. A number of studies have indicated that exposure to aluminium can impair learning and memory function. The purpose of this study was to investigate the mechanism of long-term potentiation(LTP) injury and the related signalling pathway activated by aluminium exposure. The results showed that aluminium treatment produced dose-dependent inhibition of LTP and reduced the activity of Histone H3K9 demethylation (H3K9me2) demethylase and the expression of the PHD (plant homeodomain) finger protein 8 (PHF8). Interestingly, there was no statistically significant difference in the expression of the PHF8 gene, suggesting that aluminium exposure only affects the translation process. Decrease in brain-derived neurotrophic factor (BDNF) expression may be related to the effect of aluminium. With correlation analysis between the hippocampal standardised field excitatory postsynaptic potential (fEPSP) amplitude and the expression of various proteins in the aluminium-exposed rat, the hippocampal standardised fEPSP amplitude was positively correlated with the expression of hippocampal PHF8 and BDNF proteins, and negatively correlated with the expression of hippocampal H3K9me2 protein. The correlation between H3K9me2 and BDNF was also considered negative. The results suggest that changes in synaptic plasticity might be related to changes in these proteins, which were induced by aluminium exposure. In conclusion, chronic aluminium exposure may inhibit PHF8 and prevent it from functioning as a demethylase. This may block H3K9me2 demethylation, decrease BDNF protein expression, and lead to LTP impairment.
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Affiliation(s)
- Huan Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China; Key Lab of Environmental Hazard and Health of Shanxi Province, Shanxi Medical University, China; Key Lab of Cellular Physiology of Education Ministry, Shanxi Medical University, China
| | - Xingli Xue
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China; Key Lab of Environmental Hazard and Health of Shanxi Province, Shanxi Medical University, China
| | - Zhaoyang Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China
| | - Baolong Pan
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China
| | - Yanxia Hao
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China; Key Lab of Environmental Hazard and Health of Shanxi Province, Shanxi Medical University, China
| | - Qiao Niu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, China; Key Lab of Environmental Hazard and Health of Shanxi Province, Shanxi Medical University, China; Key Lab of Cellular Physiology of Education Ministry, Shanxi Medical University, China.
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27
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Kenchanmane Raju SK, Ritter EJ, Niederhuth CE. Establishment, maintenance, and biological roles of non-CG methylation in plants. Essays Biochem 2019; 63:743-755. [PMID: 31652316 PMCID: PMC6923318 DOI: 10.1042/ebc20190032] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
Cytosine DNA methylation is prevalent throughout eukaryotes and prokaryotes. While most commonly thought of as being localized to dinucleotide CpG sites, non-CG sites can also be modified. Such non-CG methylation is widespread in plants, occurring at trinucleotide CHG and CHH (H = A, T, or C) sequence contexts. The prevalence of non-CG methylation in plants is due to the plant-specific CHROMOMETHYLASE (CMT) and RNA-directed DNA Methylation (RdDM) pathways. These pathways have evolved through multiple rounds of gene duplication and gene loss, generating epigenomic variation both within and between species. They regulate both transposable elements and genes, ensure genome integrity, and ultimately influence development and environmental responses. In these capacities, non-CG methylation influence and shape plant genomes.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
- AgBioResearch, Michigan State University, East Lansing, MI 48824, U.S.A
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29
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Wang H, Guo S, Qiao X, Guo J, Li Z, Zhou Y, Bai S, Gao Z, Wang D, Wang P, Galbraith DW, Song CP. BZU2/ZmMUTE controls symmetrical division of guard mother cell and specifies neighbor cell fate in maize. PLoS Genet 2019; 15:e1008377. [PMID: 31465456 PMCID: PMC6738654 DOI: 10.1371/journal.pgen.1008377] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/11/2019] [Accepted: 08/19/2019] [Indexed: 12/02/2022] Open
Abstract
Intercellular communication in adjacent cell layers determines cell fate and polarity, thus orchestrating tissue specification and differentiation. Here we use the maize stomatal apparatus as a model to investigate cell fate determination. Mutations in ZmBZU2 (bizui2, bzu2) confer a complete absence of subsidiary cells (SCs) and normal guard cells (GCs), leading to failure of formation of mature stomatal complexes. Nuclear polarization and actin accumulation at the interface between subsidiary mother cells (SMCs) and guard mother cells (GMCs), an essential pre-requisite for asymmetric cell division, did not occur in Zmbzu2 mutants. ZmBZU2 encodes a basic helix-loop-helix (bHLH) transcription factor, which is an ortholog of AtMUTE in Arabidopsis (BZU2/ZmMUTE). We found that a number of genes implicated in stomatal development are transcriptionally regulated by BZU2/ZmMUTE. In particular, BZU2/ZmMUTE directly binds to the promoters of PAN1 and PAN2, two early regulators of protodermal cell fate and SMC polarization, consistent with the low levels of transcription of these genes observed in bzu2-1 mutants. BZU2/ZmMUTE has the cell-to-cell mobility characteristic similar to that of BdMUTE in Brachypodium distachyon. Unexpectedly, BZU2/ZmMUTE is expressed in GMC from the asymmetric division stage to the GMC division stage, and especially in the SMC establishment stage. Taken together, these data imply that BZU2/ZmMUTE is required for early events in SMC polarization and differentiation as well as for the last symmetrical division of GMCs to produce the two GCs, and is a master determinant of the cell fate of its neighbors through cell-to-cell communication.
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Affiliation(s)
- Hongliang Wang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Siyi Guo
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xin Qiao
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Jianfei Guo
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Zuliang Li
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yusen Zhou
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shenglong Bai
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhiyong Gao
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Daojie Wang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Pengcheng Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David W. Galbraith
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
- School of Plant Sciences, the University of Arizona, Tucson, Arizona, United States of America
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
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30
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Niculite CM, Enciu AM, Hinescu ME. CD 36: Focus on Epigenetic and Post-Transcriptional Regulation. Front Genet 2019; 10:680. [PMID: 31379931 PMCID: PMC6659770 DOI: 10.3389/fgene.2019.00680] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/28/2019] [Indexed: 12/11/2022] Open
Abstract
CD36 is a transmembrane protein involved in fatty acid translocation, scavenging for oxidized fatty acids acting as a receptor for adhesion molecules. It is expressed on macrophages, as well as other types of cells, such as endothelial and adipose cells. CD36 participates in muscle lipid uptake, adipose energy storage, and gut fat absorption. Recently, several preclinical and clinical studies demonstrated that upregulation of CD36 is a prerequisite for tumor metastasis. Cancer metastasis-related research emerged much later and has been less investigated, though it is equally or even more important. CD36 protein expression can be modified by epigenetic changes and post-transcriptional interference from non-coding RNAs. Some data indicate modulation of CD36 expression in specific cell types by epigenetic changes via DNA methylation patterns or histone tails, or through miRNA interference, but this is largely unexplored. The few papers addressing this topic refer mostly to lipid metabolism-related pathologies, whereas in cancer research, data are even more scarce. The aim of this review was to summarize major epigenetic and post-transcriptional mechanisms that impact CD36 expression in relation to various pathologies while highlighting the areas in need of further exploration.
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Affiliation(s)
- Cristina-Mariana Niculite
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Ana-Maria Enciu
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Mihail Eugen Hinescu
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
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31
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Liu X, Zhao J, Guo HS. IBM1-dependent H3K9 demethylation enables self-silencing of an exogenous silencer for the non-cell autonomous silencing of an endogenous target gene. J Genet Genomics 2019; 46:149-153. [PMID: 30935857 DOI: 10.1016/j.jgg.2019.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/19/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Xiaolan Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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32
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Duan CG, Zhu JK, Cao X. Retrospective and perspective of plant epigenetics in China. J Genet Genomics 2018; 45:621-638. [PMID: 30455036 DOI: 10.1016/j.jgg.2018.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 01/21/2023]
Abstract
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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33
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Li Z, Fu X, Wang Y, Liu R, He Y. Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants. Nat Genet 2018; 50:1254-1261. [DOI: 10.1038/s41588-018-0190-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/16/2018] [Indexed: 12/14/2022]
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34
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Kim JY, Yang W, Forner J, Lohmann JU, Noh B, Noh YS. Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. EMBO J 2018; 37:embj.201798726. [PMID: 30061313 DOI: 10.15252/embj.201798726] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022] Open
Abstract
Shoot regeneration can be achieved in vitro through a two-step process involving the acquisition of pluripotency on callus-induction media (CIM) and the formation of shoots on shoot-induction media. Although the induction of root-meristem genes in callus has been noted recently, the mechanisms underlying their induction and their roles in de novo shoot regeneration remain unanswered. Here, we show that the histone acetyltransferase HAG1/AtGCN5 is essential for de novo shoot regeneration. In developing callus, it catalyzes histone acetylation at several root-meristem gene loci including WOX5, WOX14, SCR, PLT1, and PLT2, providing an epigenetic platform for their transcriptional activation. In turn, we demonstrate that the transcription factors encoded by these loci act as key potency factors conferring regeneration potential to callus and establishing competence for de novo shoot regeneration. Thus, our study uncovers key epigenetic and potency factors regulating plant-cell pluripotency. These factors might be useful in reprogramming lineage-specified plant cells to pluripotency.
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Affiliation(s)
- Ji-Yun Kim
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Woorim Yang
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Joachim Forner
- Department of Stem Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Bosl Noh
- Research Institute of Basic Sciences, Seoul National University, Seoul, Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul, Korea .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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35
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Zervudacki J, Yu A, Amesefe D, Wang J, Drouaud J, Navarro L, Deleris A. Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons. EMBO J 2018; 37:e98482. [PMID: 29871888 PMCID: PMC6043853 DOI: 10.15252/embj.201798482] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 11/09/2022] Open
Abstract
Mobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In this study, we employed an ATCOPIA93 long-terminal repeat (LTR) promoter-GUS fusion to show that this retrotransposon behaves like an immune-responsive gene during pathogen defense in Arabidopsis We also showed that the endogenous ATCOPIA93 copy "EVD", which is activated in the presence of bacterial stress, is negatively regulated by both DNA methylation and polycomb-mediated silencing, a mode of repression typically found at protein-coding and microRNA genes. Interestingly, an ATCOPIA93-derived soloLTR is located upstream of the disease resistance gene RPP4 and is devoid of DNA methylation and H3K27m3 marks. Through loss-of-function experiments, we demonstrate that this soloLTR is required for the proper expression of RPP4 during plant defense, thus linking the responsiveness of ATCOPIA93 to biotic stress and the co-option of its LTR for plant immunity.
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Affiliation(s)
- Jérôme Zervudacki
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Agnès Yu
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Delase Amesefe
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Jingyu Wang
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Jan Drouaud
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Lionel Navarro
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Angélique Deleris
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
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36
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Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Nat Genet 2018; 50:865-873. [PMID: 29736015 PMCID: PMC6317521 DOI: 10.1038/s41588-018-0115-y] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/21/2018] [Indexed: 11/09/2022]
Abstract
DNA methylation is essential for gene regulation, transposon silencing,
and imprinting. Although the generation of specific DNA methylation patterns is
critical for these processes, how methylation is regulated at individual loci
remains unclear. Here we show that a family of four putative chromatin
remodeling factors, CLASSY (CLSY) 1–4, are required for both
locus-specific and global regulation of DNA methylation in
Arabidopsis. Mechanistically, these factors act in
connection with RNA polymerase-IV (Pol-IV) to control the production of
24-nucleotide small interfering RNAs (24nt-siRNAs), which guide DNA methylation.
Individually, the CLSYs regulate Pol-IV-chromatin association and 24nt-siRNA
production at thousands of distinct loci, and together, they regulate
essentially all 24nt-siRNAs. Depending on the CLSYs involved, this regulation
relies on different repressive chromatin modifications to facilitate
locus-specific control of DNA methylation. Given the conservation between
methylation systems in plants and mammals, analogous pathways likely operate in
a broad range of organisms.
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Ramirez-Prado JS, Piquerez SJM, Bendahmane A, Hirt H, Raynaud C, Benhamed M. Modify the Histone to Win the Battle: Chromatin Dynamics in Plant-Pathogen Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:355. [PMID: 29616066 PMCID: PMC5868138 DOI: 10.3389/fpls.2018.00355] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/02/2018] [Indexed: 05/02/2023]
Abstract
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses. Herein, we review the state of the art in the epigenomic aspects of plant immunity, focusing on chromatin modifications, chromatin modifiers, and their physiological consequences. In addition, we explore the exciting field of understanding how plant pathogens have adapted to manipulate the plant epigenomic regulation in order to weaken their immune system and thrive in their host, as well as how histone modifications in eukaryotic pathogens are involved in the regulation of their virulence.
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Affiliation(s)
- Juan S. Ramirez-Prado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Sophie J. M. Piquerez
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Abdelhafid Bendahmane
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Heribert Hirt
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Cécile Raynaud
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Moussa Benhamed
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
- *Correspondence: Moussa Benhamed,
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Liu H, Zhang H, Dong YX, Hao YJ, Zhang XS. DNA METHYLTRANSFERASE1-mediated shoot regeneration is regulated by cytokinin-induced cell cycle in Arabidopsis. THE NEW PHYTOLOGIST 2018; 217:219-232. [PMID: 28960381 DOI: 10.1111/nph.14814] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/19/2017] [Indexed: 05/22/2023]
Abstract
DNA methylation plays a critical role in diverse biological processes of plants. Arabidopsis DNA METHYLTRANSFERASE1 (MET1) represses shoot regeneration by inhibiting WUSCHEL (WUS) expression, which is essential for shoot initiation. However, the upstream signals regulating MET1 expression during this process are unclear. We analyzed the signals regulating MET1 expression using a number of established strategies, such as genetic analysis, confocal microscopy, quantitative real-time PCR and chromatin immunoprecipitation. MET1 expression patterns underwent dynamic changes with the initiation of WUS during shoot regeneration. The cell cycle regulator E2FA was characterized as an upstream factor directly promoting MET1 expression. Moreover, cytokinin promoted MET1 expression partially by enhancing CYCD3 expression. Our findings reveal that MET1-mediated shoot regeneration is regulated by the cytokinin-induced cell cycle, and provide new insights into the regulation of DNA methylation in shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Hui Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Xiu Dong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
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Huang SSC, Ecker JR. Piecing together cis-regulatory networks: insights from epigenomics studies in plants. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10:e1411. [PMID: 29194997 DOI: 10.1002/wsbm.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Shao-Shan C Huang
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA
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Pelletier JM, Kwong RW, Park S, Le BH, Baden R, Cagliari A, Hashimoto M, Munoz MD, Fischer RL, Goldberg RB, Harada JJ. LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development. Proc Natl Acad Sci U S A 2017; 114:E6710-E6719. [PMID: 28739919 PMCID: PMC5559047 DOI: 10.1073/pnas.1707957114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
LEAFY COTYLEDON1 (LEC1), an atypical subunit of the nuclear transcription factor Y (NF-Y) CCAAT-binding transcription factor, is a central regulator that controls many aspects of seed development including the maturation phase during which seeds accumulate storage macromolecules and embryos acquire the ability to withstand desiccation. To define the gene networks and developmental processes controlled by LEC1, genes regulated directly by and downstream of LEC1 were identified. We compared the mRNA profiles of wild-type and lec1-null mutant seeds at several stages of development to define genes that are down-regulated or up-regulated by the lec1 mutation. We used ChIP and differential gene-expression analyses in Arabidopsis seedlings overexpressing LEC1 and in developing Arabidopsis and soybean seeds to identify globally the target genes that are transcriptionally regulated by LEC1 in planta Collectively, our results show that LEC1 controls distinct gene sets at different developmental stages, including those that mediate the temporal transition between photosynthesis and chloroplast biogenesis early in seed development and seed maturation late in development. Analyses of enriched DNA sequence motifs that may act as cis-regulatory elements in the promoters of LEC1 target genes suggest that LEC1 may interact with other transcription factors to regulate distinct gene sets at different stages of seed development. Moreover, our results demonstrate strong conservation in the developmental processes and gene networks regulated by LEC1 in two dicotyledonous plants that diverged ∼92 Mya.
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Affiliation(s)
- Julie M Pelletier
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Raymond W Kwong
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Soomin Park
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Russell Baden
- Department of Plant Biology, University of California, Davis, CA 95616
| | | | - Meryl Hashimoto
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Matthew D Munoz
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
| | - John J Harada
- Department of Plant Biology, University of California, Davis, CA 95616;
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Battilana J, Dunlevy JD, Boss PK. Histone modifications at the grapevine VvOMT3 locus, which encodes an enzyme responsible for methoxypyrazine production in the berry. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:655-664. [PMID: 32480596 DOI: 10.1071/fp16434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/16/2017] [Indexed: 05/21/2023]
Abstract
Some herbaceous characters in wine are attributed to the presence of aroma compounds collectively known as methoxypyrazines (MPs). In grape berries their formation has been hypothesised to start from a reaction of two amino acids or an amino acid and an unknown 1,2-dicarbonyl compound, leading to the formation of hydroxypyrazine, which is then enzymatically methylated to form a MP. The enzyme responsible of the formation of 3-isobutyl-2-methoxypyrazine has been recently identified as VvOMT3 whose regulation is still not understood. The concentration of MPs in grapes is known to be influenced by development, environmental stimuli and most importantly grape variety. In order to investigate the chromatin arrangement of that region a chromatin immunoprecipitation analysis has been performed and putative differences in epigenetic regulation of VvOMT3 spatially between the skin and flesh tissues and also temporally during fruit development have been detected. There are also allelic differences in VvOMT3 histone modifications which are maintained in subsequent generations. This study provides evidence of histone tail modification of the VvOMT3 locus in grapevine, which may play a role in the spatial and developmental regulation of the expression of this gene.
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Affiliation(s)
- Juri Battilana
- FEM-IASMA Genomics and Biology of Fruit Crop Department, Research and Innovation Centre - Fondazione Edmund Mach. Via E. Mach 1, 38010 - S. Michele all'Adige (TN), Italy
| | - Jake D Dunlevy
- CSIRO Agriculture and Food, PMB 2, Glen Osmond, SA 5064, Australia
| | - Paul K Boss
- CSIRO Agriculture and Food, PMB 2, Glen Osmond, SA 5064, Australia
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Chowdhury B, Cho IH, Irudayaraj J. Technical advances in global DNA methylation analysis in human cancers. J Biol Eng 2017; 11:10. [PMID: 28261325 PMCID: PMC5331624 DOI: 10.1186/s13036-017-0052-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/10/2017] [Indexed: 02/07/2023] Open
Abstract
Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types. Important breakthroughs in the recent years have uncovered further oxidized derivatives of 5mC - 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), thereby expanding our understanding of the DNA methylation dynamics. While the biological roles of these epigenetic derivatives are being extensively characterized, this review presents a perspective on the opportunity of innovation in the global methylation analysis platforms. While multiple methods for global analysis of 5mC in clinical samples exist and have been reviewed elsewhere, two of the established methods - Liquid Chromatography coupled with mass spectrometry (LC-MS/MS) and Immunoquantification have successfully evolved to include the quantitation of 5hmC, 5fC and 5caC. Although the analytical performance of LC-MS/MS is superior, the simplicity afforded by the experimental procedure of immunoquantitation ensures it’s near ubiquity in clinical applications. Recent developments in spectroscopy, nanotechnology and sequencing also provide immense promise for future evaluations and are discussed briefly. Finally, we provide a perspective on the current scenario of global DNA methylation analysis tools and present suggestions to develop the next generation toolset.
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Affiliation(s)
- Basudev Chowdhury
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, 47907 IN USA
| | - Il-Hoon Cho
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, 461-713 Republic of Korea
| | - Joseph Irudayaraj
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
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Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression mainly at the posttranscriptional level. Similar to protein-coding genes, their expression is also controlled by genetic and epigenetic mechanisms. Disruption of these control processes leads to abnormal expression of miRNAs in cancer. In this chapter, we discuss the supportive links between miRNAs and epigenetics in the context of carcinogenesis. miRNAs can be epigenetically regulated by DNA methylation and/or specific histone modifications. However, they can themselves (epi-miRNAs) repress key enzymes that drive epigenetic remodeling and also bind to complementary sequences in gene promoters, recruiting specific protein complexes that modulate chromatin structure and gene expression. All these issues affect the transcriptional landscape of cells. Most important, in the cancer clinical scenario, knowledge about miRNAs epigenetic dysregulation can not only be beneficial as a prognostic biomarker, but can also help in the design of new therapeutic approaches.
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Affiliation(s)
- Catia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain.
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44
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Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage. Proc Natl Acad Sci U S A 2016; 114:406-411. [PMID: 28028228 DOI: 10.1073/pnas.1619774114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Previously, we have shown that loss of the histone 3 lysine 27 (H3K27) monomethyltransferases ARABIDOPSIS TRITHORAX-RELATED 5 (ATXR5) and ATXR6 (ATXR6) results in the overreplication of heterochromatin. Here we show that the overreplication results in DNA damage and extensive chromocenter remodeling into unique structures we have named "overreplication-associated centers" (RACs). RACs have a highly ordered structure with an outer layer of condensed heterochromatin, an inner layer enriched in the histone variant H2AX, and a low-density core containing foci of phosphorylated H2AX (a marker of double-strand breaks) and the DNA-repair enzyme RAD51. atxr5,6 mutants are strongly affected by mutations in DNA repair, such as ATM and ATR. Because of its dense packaging and repetitive DNA sequence, heterochromatin is a challenging environment in which to repair DNA damage. Previous work in animals has shown that heterochromatic breaks are translocated out of the heterochromatic domain for repair. Our results show that atxr5,6 mutants use a variation on this strategy for repairing heterochromatic DNA damage. Rather than being moved to adjacent euchromatic regions, as in animals, heterochromatin undergoes large-scale remodeling to create a compartment with low chromatin density.
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45
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Liu H, Ma X, Han HN, Hao YJ, Zhang XS. AtPRMT5 Regulates Shoot Regeneration through Mediating Histone H4R3 Dimethylation on KRPs and Pre-mRNA Splicing of RKP in Arabidopsis. MOLECULAR PLANT 2016; 9:1634-1646. [PMID: 27780782 DOI: 10.1016/j.molp.2016.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
Protein arginine methylation plays important roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we characterized the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II protein arginine methyltransferase that methylates proteins, including histones and RNA splicing factors. The frequency of shoot regeneration and the number of shoots per callus were decreased in the atprmt5 mutant compared with those in the wild type. Chromatin immunoprecipitation analysis revealed that AtPRMT5 targets KIP-RELATED PROTEINs (KRPs), which encode the cyclin-dependent kinase inhibitors that repress the cell cycle. During shoot regeneration, the KRP transcript level increased in the atprmt5 mutant, which resulted from reduced histone H4R3 methylation in the KRP promoter. Overexpression of KRP significantly reduced the frequency of shoot regeneration and shoot number per callus. Furthermore, abnormal pre-mRNA splicing in the gene RELATED TO KPC1 (RKP), which encodes an ubiquitin E3 ligase, was detected in the atprmt5 mutant. RKP functions in regulating KRP protein degradation, and mutation in RKP inhibited shoot regeneration. Thus, AtPRMT5 regulated shoot regeneration through histone modification-mediated KRP transcription and RKP pre-mRNA splicing. Our findings provide new insights into the function of protein arginine methylation in de novo shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xu Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Hua Nan Han
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China.
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Knockdown of WHIRLY1 Affects Drought Stress-Induced Leaf Senescence and Histone Modifications of the Senescence-Associated Gene HvS40. PLANTS 2016; 5:plants5030037. [PMID: 27608048 PMCID: PMC5039745 DOI: 10.3390/plants5030037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 01/02/2023]
Abstract
The plastid-nucleus located protein WHIRLY1 has been described as an upstream regulator of leaf senescence, binding to the promoter of senescence-associated genes like HvS40. To investigate the impact of WHIRLY1 on drought stress-induced, premature senescence, transgenic barley plants with an RNAi-mediated knockdown of the HvWHIRLY1 gene were grown under normal and drought stress conditions. The course of leaf senescence in these lines was monitored by physiological parameters and studies on the expression of senescence- and drought stress-related genes. Drought treatment accelerated leaf senescence in WT plants, whereas WHIRLY 1 knockdown lines (RNAi-W1) showed a stay-green phenotype. Expression of both senescence-associated and drought stress-responsive genes, was delayed in the transgenic plants. Notably, expression of transcription factors of the WRKY and NAC families, which are known to function in senescence- and stress-related signaling pathways, was affected in plants with impaired accumulation of WHIRLY1, indicating that WHIRLY1 acts as an upstream regulator of drought stress-induced senescence. To reveal the epigenetic indexing of HvS40 at the onset of drought-induced senescence in WT and RNAi-W1 lines, stress-responsive loading with histone modifications of promoter and coding sequences of HvS40 was analyzed by chromatin immunoprecipitation and quantified by qRT-PCR. In the wildtype, the euchromatic mark H3K9ac of the HvS40 gene was low under control conditions and was established in response to drought treatment, indicating the action of epigenetic mechanisms in response to drought stress. However, drought stress caused no significant increase in H3K9ac in plants impaired in accumulation of WHIRLY1. The results show that WHIRLY1 knockdown sets in motion a delay in senescence that involves all aspects of gene expression, including changes in chromatin structure.
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Niederhuth CE, Schmitz RJ. Putting DNA methylation in context: from genomes to gene expression in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:149-156. [PMID: 27590871 DOI: 10.1016/j.bbagrm.2016.08.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 12/26/2022]
Abstract
Plant DNA methylation is its own language, interpreted by the cell to maintain silencing of transposons, facilitate chromatin structure, and to ensure proper expression of some genes. Just as in any language, context is important. Rather than being a simple "on-off switch", DNA methylation has a range of "meanings" dependent upon the underlying sequence and its location in the genome. Differences in the sequence context of individual sites are established, maintained, and interpreted by differing molecular pathways. Varying patterns of methylation within genes and surrounding sequences are associated with a continuous range of expression differences, from silencing to constitutive expression. These often-subtle differences have been pieced together from years of effort, but have taken off with the advent of methods for assessing methylation across entire genomes. Recognizing these patterns and identifying underlying causes is essential for understanding the function of DNA methylation and its systems-wide contribution to a range of processes in plant genomes. 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)
- Chad E Niederhuth
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, The University of Georgia, Athens, GA, 30602, USA.
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Wendte JM, Pikaard CS. The RNAs of RNA-directed DNA methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:140-148. [PMID: 27521981 DOI: 10.1016/j.bbagrm.2016.08.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5' and 3' ends. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks. 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)
- Jered M Wendte
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.
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Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin. J Virol 2016; 90:7529-7540. [PMID: 27279611 DOI: 10.1128/jvi.00656-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In plants, RNA-directed DNA methylation (RdDM) employs small RNAs to target enzymes that methylate cytosine residues. Cytosine methylation and dimethylation of histone 3 lysine 9 (H3K9me2) are often linked. Together they condition an epigenetic defense that results in chromatin compaction and transcriptional silencing of transposons and viral chromatin. Canonical RdDM (Pol IV-RdDM), involving RNA polymerases IV and V (Pol IV and Pol V), was believed to be necessary to establish cytosine methylation, which in turn could recruit H3K9 methyltransferases. However, recent studies have revealed that a pathway involving Pol II and RNA-dependent RNA polymerase 6 (RDR6) (RDR6-RdDM) is likely responsible for establishing cytosine methylation at naive loci, while Pol IV-RdDM acts to reinforce and maintain it. We used the geminivirus Beet curly top virus (BCTV) as a model to examine the roles of Pol IV and Pol V in establishing repressive viral chromatin methylation. As geminivirus chromatin is formed de novo in infected cells, these viruses are unique models for processes involved in the establishment of epigenetic marks. We confirm that Pol IV and Pol V are not needed to establish viral DNA methylation but are essential for its amplification. Remarkably, however, both Pol IV and Pol V are required for deposition of H3K9me2 on viral chromatin. Our findings suggest that cytosine methylation alone is not sufficient to trigger de novo deposition of H3K9me2 and further that Pol IV-RdDM is responsible for recruiting H3K9 methyltransferases to viral chromatin. IMPORTANCE In plants, RNA-directed DNA methylation (RdDM) uses small RNAs to target cytosine methylation, which is often linked to H3K9me2. These epigenetic marks silence transposable elements and DNA virus genomes, but how they are established is not well understood. Canonical RdDM, involving Pol IV and Pol V, was thought to establish cytosine methylation that in turn could recruit H3K9 methyltransferases, but recent studies compel a reevaluation of this view. We used BCTV to investigate the roles of Pol IV and Pol V in chromatin methylation. We found that both are needed to amplify, but not to establish, DNA methylation. However, both are required for deposition of H3K9me2. Our findings suggest that cytosine methylation is not sufficient to recruit H3K9 methyltransferases to naive viral chromatin and further that Pol IV-RdDM is responsible.
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