1
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Harkess A, Bewick AJ, Lu Z, Fourounjian P, Michael TP, Schmitz RJ, Meyers BC. The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza. G3 (Bethesda) 2024; 14:jkae004. [PMID: 38190722 PMCID: PMC10989885 DOI: 10.1093/g3journal/jkae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.
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Affiliation(s)
- Alex Harkess
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Paul Fourounjian
- Waksman Institute of Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Todd P Michael
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- Division of Plant Sciences, University of Missouri—Columbia, Columbia, MO 65211, USA
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2
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Yadav S, Meena S, Kalwan G, Jain PK. DNA methylation: an emerging paradigm of gene regulation under drought stress in plants. Mol Biol Rep 2024; 51:311. [PMID: 38372841 DOI: 10.1007/s11033-024-09243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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3
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Lee J, Lee S, Park K, Shin SY, Frost JM, Hsieh PH, Shin C, Fischer RL, Hsieh TF, Choi Y. Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis. Front Plant Sci 2023; 14:1204279. [PMID: 37360705 PMCID: PMC10285158 DOI: 10.3389/fpls.2023.1204279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
CHH methylation (mCHH) increases gradually during embryogenesis across dicotyledonous plants, indicating conserved mechanisms of targeting and conferral. Although it is suggested that methylation increase during embryogenesis enhances transposable element silencing, the detailed epigenetic pathways underlying this process remain unclear. In Arabidopsis, mCHH is regulated by both small RNA-dependent DNA methylation (RdDM) and RNA-independent Chromomethylase 2 (CMT2) pathways. Here, we conducted DNA methylome profiling at five stages of Arabidopsis embryogenesis, and classified mCHH regions into groups based on their dependency on different methylation pathways. Our analysis revealed that the gradual increase in mCHH in embryos coincided with the expansion of small RNA expression and regional mCHH spreading to nearby sites at numerous loci. We identified distinct methylation dynamics in different groups of mCHH targets, which vary according to transposon length, location, and cytosine frequency. Finally, we highlight the characteristics of transposable element loci that are targeted by different mCHH machinery, showing that short, heterochromatic TEs with lower mCHG levels are enriched in loci that switch from CMT2 regulation in leaves, to RdDM regulation during embryogenesis. Our findings highlight the interplay between the length, location, and cytosine frequency of transposons and the mCHH machinery in modulating mCHH dynamics during embryogenesis.
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Affiliation(s)
- Jaehoon Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sang-Yoon Shin
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jennifer M. Frost
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Ping-Hung Hsieh
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Chanseok Shin
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
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4
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Sasaki T, Kato K, Hosaka A, Fu Y, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T. Arms race between anti-silencing and RdDM in noncoding regions of transposable elements. EMBO Rep 2023:e56678. [PMID: 37272687 PMCID: PMC10398659 DOI: 10.15252/embr.202256678] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/06/2023] Open
Abstract
Transposable elements (TEs) are among the most dynamic parts of genomes. Since TEs are potentially deleterious, eukaryotes silence them through epigenetic mechanisms such as repressive histone modifications and DNA methylation. We previously reported that Arabidopsis TEs, called VANDALs, counteract epigenetic silencing through a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to noncoding regions of specific VANDAL copies and induce loss of silent chromatin marks. The VANC-target regions form tandem repeats, which diverge rapidly. Sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here, we show that RNA-directed DNA methylation (RdDM) efficiently targets noncoding regions of VANDAL TEs to silence them de novo. Thus, escape from RdDM could be a primary event leading to the rapid evolution and diversification of sequence-specific anti-silencing systems. We propose that this selfish behavior of TEs paradoxically could make them diverse and less harmful to the host.
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Affiliation(s)
| | - Kae Kato
- National Institute of Genetics, Mishima, Japan
| | - Aoi Hosaka
- National Institute of Genetics, Mishima, Japan
| | - Yu Fu
- National Institute of Genetics, Mishima, Japan
| | | | - Asao Fujiyama
- National Institute of Genetics, Mishima, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Yoshiaki Tarutani
- National Institute of Genetics, Mishima, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Tetsuji Kakutani
- The University of Tokyo, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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5
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Kuhlmann M, Jiang H, Catoni M, Johannes F. Editorial: DNA methylation in plants associated with abiotic stress, volume II. Front Plant Sci 2023; 14:1203806. [PMID: 37293678 PMCID: PMC10244784 DOI: 10.3389/fpls.2023.1203806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Markus Kuhlmann
- Department Molecular Genetics, RG Heterosis Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hua Jiang
- Independent Research Group Applied Chromosome Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Frank Johannes
- Department Molecular Life Sciences, Research Group Population Epigenetics & Epigenomics Technical University of Munich, Munich, Germany
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6
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Arce AL, Mencia R, Cambiagno DA, Lang PL, Liu C, Burbano HA, Weigel D, Manavella PA. Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana. Cell Rep 2023; 42:112029. [PMID: 36689329 DOI: 10.1016/j.celrep.2023.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023] Open
Abstract
Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable element (TE)-derived inverted repeats (IRs) are commonly found near genes, where they affect host gene expression. However, the molecular mechanisms of such regulation are unclear in most cases. Expression of these IRs is associated with production of 24-nt small RNAs, methylation of the IRs, and drastic changes in local 3D chromatin organization. Notably, many of these IRs differ between Arabidopsis thaliana accessions, causing variation in short-range chromatin interactions and gene expression. CRISPR-Cas9-mediated disruption of two IRs leads to a switch in genome topology and gene expression with phenotypic consequences. Our data show that insertion of an IR near a gene provides an anchor point for chromatin interactions that profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.
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Affiliation(s)
- Agustín L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Patricia L Lang
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - Hernán A Burbano
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Centre for Life's Origins and Evolution, University College London, London, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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7
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Akinmusola RY, Wilkins CA, Doughty J. DDM1-Mediated TE Silencing in Plants. Plants (Basel) 2023; 12:437. [PMID: 36771522 PMCID: PMC9919755 DOI: 10.3390/plants12030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic modifications are indispensable for regulating gene bodies and TE silencing. DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeller involved in histone modifications and DNA methylation. Apart from maintaining the epigenome, DDM1 also maintains key plant traits such as flowering time and heterosis. The role of DDM1 in epigenetic regulation is best characterised in plants, especially arabidopsis, rice, maize and tomato. The epigenetic changes induced by DDM1 establish the stable inheritance of many plant traits for at least eight generations, yet DDM1 does not methylate protein-coding genes. The DDM1 TE silencing mechanism is distinct and has evolved independently of other silencing pathways. Unlike the RNA-directed DNA Methylation (RdDM) pathway, DDM1 does not depend on siRNAs to enforce the heterochromatic state of TEs. Here, we review DDM1 TE silencing activity in the RdDM and non-RdDM contexts. The DDM1 TE silencing machinery is strongly associated with the histone linker H1 and histone H2A.W. While the linker histone H1 excludes the RdDM factors from methylating the heterochromatin, the histone H2A.W variant prevents TE mobility. The DDM1-H2A.W strategy alone silences nearly all the mobile TEs in the arabidopsis genome. Thus, the DDM1-directed TE silencing essentially preserves heterochromatic features and abolishes mobile threats to genome stability.
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8
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Xiang R, Ahmad B, Liang C, Shi X, Yang L, Du G, Wang L. Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes. Front Plant Sci 2022; 13:1089392. [PMID: 36570893 PMCID: PMC9780290 DOI: 10.3389/fpls.2022.1089392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in plants and mediates transcriptional silencing by siRNAs. Different gene families have role in the regulation of the RdDM pathway and there is a lack of information about these gene families in the grapes (Vitis vinifera L.). Here, we mentioned the genome-wide identification, bioinformatics analysis, evolutionary history, and expression profiling of VvRdDM pathway genes against various stresses, hormonal treatments as well as in different organs. Sixty VvRdDM genes belonging to fourteen different families were identified. All the genes were unevenly distributed and chromosome 4 contained the highest number of genes (7). Most of the genes showed similar exon-intron and motif distribution patterns within the same subfamilies. Out of 14 families, only members of 4 families underwent duplication events during the evolutionary process and 50% of members of the AGO family are the result of duplication events. Based on Ka/Ks ratio all duplicated gene pairs have a negative mode of selection. VvRdDM pathway genes showed differential spatiotemporal expression patterns against different hormone and stress treatments. Further, with multiple transcriptome analysis, some VvRdDM genes showed a broad spectrum of high expression in different organs at various stages, and VvRdDM genes also displayed different expression in seeded and seedless cultivars during different phases of seed development. This proposed that VvRdDM genes may play multiple roles in grape growth and development, especially in seed development. qRT-PCR analysis of selected genes further verified the critical roles of RdDM genes in multiple biological processes, especially in seed development/ovule abortion i.e., VvIDN2a, VvDRD1a, VvRDR1a, and VvRDR6. Our study provides detailed information about VvRdDM genes in perspective of gene structure and evolution, as well as expression pattern against different stress, hormones and in different plants parts. It provides new candidate gene resources for further functional characterization and molecular breeding of grapes.
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Affiliation(s)
- Rui Xiang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bilal Ahmad
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Department of Horticulture, Muhammad Nawaz Sharif (MNS)-University of Agriculture Multan, Multan, Pakistan
| | - Chen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaoxin Shi
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lili Yang
- Shijiazhuang Fruit Research Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Guoqiang Du
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Li Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
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9
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Jagić M, Vuk T, Škiljaica A, Markulin L, Vičić Bočkor V, Tokić M, Miškec K, Razdorov G, Habazin S, Šoštar M, Weber I, Bauer N, Leljak Levanić D. BPM1 regulates RdDM-mediated DNA methylation via a cullin 3 independent mechanism. Plant Cell Rep 2022; 41:2139-2157. [PMID: 36066603 DOI: 10.1007/s00299-022-02911-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
BPM1 interacts with components of the DDR complex and stimulates DNA methylation at CHH sites, suggesting its involvement in the RdDM methylation pathway. The best-known function of MATH-BTB proteins, including Arabidopsis BPM proteins, is their role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin-proteasome pathway. This paper reports a new CUL3-independent role of BPM1 in RNA-directed DNA methylation (RdDM). Using quantitative and qualitative Y2H, pull down, microscale thermophoresis and FRET-FLIM, we demonstrate that BPM1 interacts with DMS3 and RDM1, components of the chromatin remodeling DDR complex involved in the recruitment of the RdDM methylation machinery. All three proteins colocalized predominantly in the nucleus. The MATH domain, which specifically binds proteins destined for degradation, was not essential for interactions with DMS3 and RDM1. In plants overexpressing BPM1, endogenous DMS3 protein levels were stable, indicating that BPM1 does not induce proteasomal degradation. In RDM1-overexpressing plants, RDM1 was not ubiquitinated. Together, these results suggest that BPM1 does not mediate the degradation of DMS3 and RDM1. Additionally, overexpression of BPM1 caused increased global methylation levels as well as CHH methylation in promoters of two RdDM-regulated genes, FWA and CML41. Overall, BPM1 seems to have a stimulating effect on RdDM activity, and this role appears to be unrelated to its known function as a Cul3-based E3 ligase adaptor.
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Affiliation(s)
- Mateja Jagić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Tamara Vuk
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Andreja Škiljaica
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Markulin
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Vedrana Vičić Bočkor
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mirta Tokić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Karlo Miškec
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | | | - Marko Šoštar
- Division of Molecular Biology, Institute Ruđer Bošković, Zagreb, Croatia
| | - Igor Weber
- Division of Molecular Biology, Institute Ruđer Bošković, Zagreb, Croatia
| | - Nataša Bauer
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Dunja Leljak Levanić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.
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10
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Fonouni-Farde C, Christ A, Blein T, Legascue MF, Ferrero L, Moison M, Lucero L, Ramírez-Prado JS, Latrasse D, Gonzalez D, Benhamed M, Quadrana L, Crespi M, Ariel F. The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants. Genome Biol 2022; 23:181. [PMID: 36038910 PMCID: PMC9422110 DOI: 10.1186/s13059-022-02750-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/17/2022] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. RESULTS Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner. CONCLUSIONS Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
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Affiliation(s)
- Camille Fonouni-Farde
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Thomas Blein
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - María Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Lucía Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Michaël Moison
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Juan Sebastián Ramírez-Prado
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Daniel Gonzalez
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Leandro Quadrana
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.,Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, 91405, Orsay, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
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11
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Liu S, Bao Y, Deng H, Liu G, Han Y, Wu Y, Zhang T, Chen C. The Methylation Inhibitor 5-Aza-2'-Deoxycytidine Induces Genome-Wide Hypomethylation in Rice. Rice (N Y) 2022; 15:35. [PMID: 35779161 PMCID: PMC9250569 DOI: 10.1186/s12284-022-00580-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation is a conserved epigenetic modification which is vital for regulating gene expression and maintaining genome stability in both mammals and plants. Homozygous mutation of rice methyltransferase 1 (met1) gene can cause host death in rice, making it difficult to obtain plant material needed for hypomethylation research. To circumvent this challenge, the methylation inhibitor, 5-Aza-2'-deoxycytidine (AzaD), is used as a cytosine nucleoside analogue to reduce genome wide hypomethylation and is widely used in hypomethylation research. However, how AzaD affects plant methylation profiles at the genome scale is largely unknown. Here, we treated rice seedlings with AzaD and compared the AzaD treatment with osmet1-2 mutants, illustrating that there are similar CG hypomethylation and distribution throughout the whole genome. Along with global methylation loss class I transposable elements (TEs) which are farther from genes compared with class II TEs, were more significantly activated, and the RNA-directed DNA Methylation (RdDM) pathway was activated in specific genomic regions to compensate for severe CG loss. Overall, our results suggest that AzaD is an effective DNA methylation inhibitor that can influence genome wide methylation and cause a series of epigenetic variations.
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Affiliation(s)
- Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Hui Deng
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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12
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Watcharanurak P, Mutirangura A. Human RNA-directed DNA methylation methylates high-mobility group box 1 protein-produced DNA gaps. Epigenomics 2022; 14:741-756. [PMID: 35762252 DOI: 10.2217/epi-2022-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background: DNA sequences around HMGB1-produced DNA gaps are hypermethylates. DNA methylation of interspersed repetitive sequences (IRS) such as Alu elements can be established through AGO4-mediating, RNA-directed DNA methylation (RdDM). HMGB1 depletion, DNA gap reduction and global hypomethylation promote genomic instability. Methods: HMGB1, SIRT1, AGO4 and DNA gap colocalizations were evaluated. Then, Alu methylation was analyzed in HMGB1-deficient or HMGB1-overexpressing cells and Alu siRNA-transfected HMGB1-deficient cells. Results: HMGB1, SIRT1, AGO4 and DNA gap are colocalized in the nucleus. Moreover, HMGB1 or Alu siRNA increased Alu methylation, whereas Alu siRNA could not methylate HMGB1-deficient cells. Conclusion: AGO4 play a role in methylating DNA sequence around HMGB1-produced DNA gaps and localize DNA gap in IRS, and loss of intranuclear HMGB1 causes global hypomethylation.
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Affiliation(s)
- Papitchaya Watcharanurak
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer & Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer & Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
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13
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Bianchetti R, Bellora N, de Haro LA, Zuccarelli R, Rosado D, Freschi L, Rossi M, Bermudez L. Phytochrome-Mediated Light Perception Affects Fruit Development and Ripening Through Epigenetic Mechanisms. Front Plant Sci 2022; 13:870974. [PMID: 35574124 PMCID: PMC9096621 DOI: 10.3389/fpls.2022.870974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Phytochrome (PHY)-mediated light and temperature perception has been increasingly implicated as important regulator of fruit development, ripening, and nutritional quality. Fruit ripening is also critically regulated by chromatin remodeling via DNA demethylation, though the molecular basis connecting epigenetic modifications in fruits and environmental cues remains largely unknown. Here, to unravel whether the PHY-dependent regulation of fruit development involves epigenetic mechanisms, an integrative analysis of the methylome, transcriptome and sRNAome of tomato fruits from phyA single and phyB1B2 double mutants was performed in immature green (IG) and breaker (BK) stages. The transcriptome analysis showed that PHY-mediated light perception regulates more genes in BK than in the early stages of fruit development (IG) and that PHYB1B2 has a more substantial impact than PHYA in the fruit transcriptome, in both analyzed stages. The global profile of methylated cytosines revealed that both PHYA and PHYB1B2 affect the global methylome, but PHYB1B2 has a greater impact on ripening-associated methylation reprogramming across gene-rich genomic regions in tomato fruits. Remarkably, promoters of master ripening-associated transcription factors (TF) (RIN, NOR, CNR, and AP2a) and key carotenoid biosynthetic genes (PSY1, PDS, ZISO, and ZDS) remained highly methylated in phyB1B2 from the IG to BK stage. The positional distribution and enrichment of TF binding sites were analyzed over the promoter region of the phyB1B2 DEGs, exposing an overrepresentation of binding sites for RIN as well as the PHY-downstream effectors PIFs and HY5/HYH. Moreover, phyA and phyB1B2 mutants showed a positive correlation between the methylation level of sRNA cluster-targeted genome regions in gene bodies and mRNA levels. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes, and remodeling factors) and transcriptional regulators leading to altered mRNA profile of ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.
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Affiliation(s)
- Ricardo Bianchetti
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET), Bariloche, Argentina
| | - Luis A. de Haro
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Zuccarelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Daniele Rosado
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luisa Bermudez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, INTA-CONICET, Castelar, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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14
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Wang L, Xu D, Scharf K, Frank W, Leister D, Kleine T. The RNA-binding protein RBP45D of Arabidopsis promotes transgene silencing and flowering time. Plant J 2022; 109:1397-1415. [PMID: 34919766 DOI: 10.1111/tpj.15637] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
RNA-directed DNA methylation (RdDM) helps to defend plants against invasive nucleic acids. In the canonical form of RdDM, 24-nt small interfering RNAs (siRNAs) are produced by DICER-LIKE 3 (DCL3). The siRNAs are loaded onto ARGONAUTE (AGO) proteins leading ultimately to de novo DNA methylation. Here, we introduce the Arabidopsis thaliana prors1 (LUC) transgenic system, in which 24-nt siRNAs are generated to silence the promoter-LUC construct. A forward genetic screen performed with this system identified, besides known components of RdDM (NRPD2A, RDR2, AGO4 and AGO6), the RNA-binding protein RBP45D. RBP45D is involved in CHH (where H is A, C or T) DNA methylation, and maintains siRNA production originating from the LUC transgene. RBP45D is localized to the nucleus, where it is associated with small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). RNA-Seq analysis showed that in CRISPR/Cas-mediated rbp-ko lines FLOWERING LOCUS C (FLC) mRNA levels are upregulated and several loci differentially spliced, among them FLM. In consequence, loss of RBP45D delays flowering, presumably mediated by the release of FLC levels and/or alternative splicing of FLM. Moreover, because levels and processing of transcripts of known RdDM genes are not altered in rbp-ko lines, RBP45D should have a more direct function in transgene silencing, probably independent of the canonical RdDM pathway. We suggest that RBP45D facilitates siRNA production by stabilizing either the precursor RNA or the slicer protein. Alternatively, RBP45D could be involved in chromatin modifications, participate in retention of Pol IV transcripts and/or in Pol V-dependent lncRNA retention in chromatin to enable their scaffold function.
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Affiliation(s)
- Liangsheng Wang
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Duorong Xu
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Kristin Scharf
- Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
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15
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Petrella R, Cucinotta M, Mendes MA, Underwood CJ, Colombo L. The emerging role of small RNAs in ovule development, a kind of magic. Plant Reprod 2021; 34:335-351. [PMID: 34142243 PMCID: PMC8566443 DOI: 10.1007/s00497-021-00421-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/08/2021] [Indexed: 05/03/2023]
Abstract
In plants, small RNAs have been recognized as key genetic and epigenetic regulators of development. Small RNAs are usually 20 to 30 nucleotides in length and they control, in a sequence specific manner, the transcriptional or post-transcriptional expression of genes. In this review, we present a comprehensive overview of the most recent findings about the function of small RNAs in ovule development, including megasporogenesis and megagametogenesis, both in sexual and apomictic plants. We discuss recent studies on the role of miRNAs, siRNAs and trans-acting RNAs (ta-siRNAs) in early female germline differentiation. The mechanistic complexity and unique regulatory features are reviewed, and possible directions for future research are provided.
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Affiliation(s)
- Rosanna Petrella
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Mara Cucinotta
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Marta A Mendes
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
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16
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Atsumi G, Matsuo K, Fukuzawa N, Matsumura T. Virus-Mediated Targeted DNA Methylation Illuminates the Dynamics of Methylation in an Endogenous Plant Gene. Int J Mol Sci 2021; 22:4125. [PMID: 33923780 PMCID: PMC8073618 DOI: 10.3390/ijms22084125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation maintains genome stability and regulates gene expression in plants. RNA-directed DNA methylation (RdDM) is critical for appropriate methylation. However, no efficient tools are available for the investigation of the functions of specific DNA methylation. In this study, the cucumber mosaic virus vector was used for targeted DNA methylation. Methylation was rapidly induced but gradually decreased from the 3' end of the target endogenous sequence in Nicotiana benthamiana, suggesting a mechanism to protect against the ectopic introduction of DNA methylation. Increasing 24-nt siRNAs blocked this reduction in methylation by down-regulating DCL2 and DCL4. RdDM relies on the sequence identity between RNA and genomic DNA; however, this identity does not appear to be the sole determinant for efficient DNA methylation. The current findings provide new insight into the regulation of DNA methylation and promote additional effort to develop efficient targeted DNA methylation in plants.
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17
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Markulin L, Škiljaica A, Tokić M, Jagić M, Vuk T, Bauer N, Leljak Levanić D. Taking the Wheel - de novo DNA Methylation as a Driving Force of Plant Embryonic Development. Front Plant Sci 2021; 12:764999. [PMID: 34777448 PMCID: PMC8585777 DOI: 10.3389/fpls.2021.764999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 05/16/2023]
Abstract
During plant embryogenesis, regardless of whether it begins with a fertilized egg cell (zygotic embryogenesis) or an induced somatic cell (somatic embryogenesis), significant epigenetic reprogramming occurs with the purpose of parental or vegetative transcript silencing and establishment of a next-generation epigenetic patterning. To ensure genome stability of a developing embryo, large-scale transposon silencing occurs by an RNA-directed DNA methylation (RdDM) pathway, which introduces methylation patterns de novo and as such potentially serves as a global mechanism of transcription control during developmental transitions. RdDM is controlled by a two-armed mechanism based around the activity of two RNA polymerases. While PolIV produces siRNAs accompanied by protein complexes comprising the methylation machinery, PolV produces lncRNA which guides the methylation machinery toward specific genomic locations. Recently, RdDM has been proposed as a dominant methylation mechanism during gamete formation and early embryo development in Arabidopsis thaliana, overshadowing all other methylation mechanisms. Here, we bring an overview of current knowledge about different roles of DNA methylation with emphasis on RdDM during plant zygotic and somatic embryogenesis. Based on published chromatin immunoprecipitation data on PolV binding sites within the A. thaliana genome, we uncover groups of auxin metabolism, reproductive development and embryogenesis-related genes, and discuss possible roles of RdDM at the onset of early embryonic development via targeted methylation at sites involved in different embryogenesis-related developmental mechanisms.
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18
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Mendes MA, Petrella R, Cucinotta M, Vignati E, Gatti S, Pinto SC, Bird DC, Gregis V, Dickinson H, Tucker MR, Colombo L. The RNA-dependent DNA methylation pathway is required to restrict SPOROCYTELESS/NOZZLE expression to specify a single female germ cell precursor in Arabidopsis. Development 2020; 147:dev194274. [PMID: 33158925 PMCID: PMC7758631 DOI: 10.1242/dev.194274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022]
Abstract
In higher plants, the female germline is formed from the megaspore mother cell (MMC), a single cell in the premeiotic ovule. Previously, it was reported that mutants in the RNA-dependent DNA methylation (RdDM) pathway might be involved in restricting the female germline to a single nucellus cell. We show that the DRM methyltransferase double mutant drm1drm2 also presents ectopic enlarged cells, consistent with supernumerary MMC-like cells. In wild-type ovules, MMC differentiation requires SPOROCYTELESS/NOZZLE (SPL/NZZ), as demonstrated by the spl/nzz mutant failing to develop an MMC. We address the poorly understood upstream regulation of SPL/NZZ in ovules, showing that the RdDM pathway is important to restrict SPL/NZZ expression. In ago9, rdr6 and drm1drm2 mutants, SPL/NZZ is expressed ectopically, suggesting that the multiple MMC-like cells observed might be attributable to the ectopic expression of SPL/NZZ. We show that the ovule identity gene, SEEDSTICK, directly regulates AGO9 and RDR6 expression in the ovule and therefore indirectly regulates SPL/NZZ expression. A model is presented describing the network required to restrict SPL/NZZ expression to specify a single MMC.
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Affiliation(s)
- Marta A Mendes
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Rosanna Petrella
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Mara Cucinotta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Edoardo Vignati
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Stefano Gatti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sara C Pinto
- LAQV REQUIMTE, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Dayton C Bird
- School of Agriculture, Food, and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Hugh Dickinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Matthew R Tucker
- School of Agriculture, Food, and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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19
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Chen X, Xu X, Shen X, Li H, Zhu C, Chen R, Munir N, Zhang Z, Chen Y, Xuhan X, Lin Y, Lai Z. Genome-wide investigation of DNA methylation dynamics reveals a critical role of DNA demethylation during the early somatic embryogenesis of Dimocarpus longan Lour. Tree Physiol 2020; 40:1807-1826. [PMID: 32722792 DOI: 10.1093/treephys/tpaa097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 05/23/2023]
Abstract
DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing and transcriptome sequencing analyses for embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine content in EC, ICpEC and GE was 24.59, 19.65 and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene ontology and Kyoto encyclopedia of genes and genomes analysis of hypomethylated-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine treatment in EC promoted the formation of GE and enhanced the capability of longan SE. Our results suggest that DNA demethylation has important roles in longan SE development.
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Affiliation(s)
- Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Shen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hansheng Li
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- School of Resources and Chemical Engineering, Sanming University, Sanming 365000, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rongzhu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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20
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Tsuzuki M, Sethuraman S, Coke AN, Rothi MH, Boyle AP, Wierzbicki AT. Broad noncoding transcription suggests genome surveillance by RNA polymerase V. Proc Natl Acad Sci U S A 2020; 117:30799-804. [PMID: 33199612 DOI: 10.1073/pnas.2014419117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. In Arabidopsis thaliana, RNA polymerase V (Pol V) produces noncoding transcripts, which base pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets, Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of nonconserved sequences may serve an essential role in maintenance of genome integrity.
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21
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Leone M, Zavallo D, Venturuzzi A, Asurmendi S. RdDM pathway components differentially modulate Tobamovirus symptom development. Plant Mol Biol 2020; 104:467-481. [PMID: 32813230 DOI: 10.1007/s11103-020-01051-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The crop yield losses induced by phytoviruses are mainly associated with the symptoms of the disease. DNA modifications as methylation can modulate the information coded by the sequence, process named epigenetics. Viral infection can change the expression patterns of different genes linked to defenses and symptoms. This work represents the initial step to expose the role of epigenetic process, in the production of symptoms associated with plants-virus interactions. Small RNAs (sRNAs) are important molecules for gene regulation in plants and play an essential role in plant-pathogen interactions. Researchers have evaluated the relationship between viral infections as well as the endogenous accumulation of sRNAs and the transcriptional changes associated with the production of symptoms, but little is known about a possible direct role of epigenetics, mediated by 24-nt sRNAs, in the induction of these symptoms. Using different RNA directed DNA methylation (RdDM) pathway mutants and a triple demethylase mutant; here we demonstrate that the disruption of RdDM pathway during viral infection produce alterations in the plant transcriptome and in consequence changes in plant symptoms. This study represents the initial step in exposing that DNA methylation directed by endogenous sRNAs has an important role, uncoupled to defense, in the production of symptoms associated with plant-virus interactions.
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Affiliation(s)
- Melisa Leone
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
- Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Buenos Aires, Argentina
| | - Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Andrea Venturuzzi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De Los Reseros y N. Repetto S/N, Hurlingham, B1686IGC, Buenos Aires, Argentina.
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22
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Hayashi Y, Takehira K, Nozawa K, Suzuki T, Masuta Y, Kato A, Ito H. ONSEN shows different transposition activities in RdDM pathway mutants. Genes Genet Syst 2020; 95:183-190. [PMID: 32893196 DOI: 10.1266/ggs.20-00019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Most transposable elements (TEs) are tightly regulated by epigenetic mechanisms such as DNA methylation. RNA-directed DNA methylation (RdDM) is a major control mechanism of TE silencing in plants. We analyzed the transposition activity of a heat-responsive retrotransposon, ONSEN, in Arabidopsis thaliana. Transgenerational transposition was observed in RdDM pathway-deficient mutants upon heat stress. The transposition frequency was higher in the mutants of the upstream processes, but lower in the mutants of the downstream steps, of RdDM. The transposition frequency was not associated with the number of extrachromosomal ONSEN copies. Constitutive heterochromatin of interphase nuclei was dispersed upon heat stress. The degree of decondensation was higher in the RdDM mutants than in wild-type plants subjected to heat stress. We discuss the possible role of RdDM in the regulation of ONSEN transposition upon heat stress.
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Affiliation(s)
- Yui Hayashi
- Graduate School of Life Science, Hokkaido University
| | | | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University
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23
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Jiang S, Wang N, Chen M, Zhang R, Sun Q, Xu H, Zhang Z, Wang Y, Sui X, Wang S, Fang H, Zuo W, Su M, Zhang J, Fei Z, Chen X. Methylation of MdMYB1 locus mediated by RdDM pathway regulates anthocyanin biosynthesis in apple. Plant Biotechnol J 2020; 18:1736-1748. [PMID: 31930634 PMCID: PMC7336386 DOI: 10.1111/pbi.13337] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 01/05/2020] [Indexed: 05/07/2023]
Abstract
Methylation at the MdMYB1 promoter in apple sports has been reported as a regulator of the anthocyanin pathway, but little is known about how the locus is recognized by the methylation machinery to regulate anthocyanin accumulation. In this study, we analysed three differently coloured 'Fuji' apples and found that differences in the transcript levels of MdMYB1, which encodes a key regulator of anthocyanin biosynthesis, control the anthocyanin content (and therefore colour) in fruit skin. The CHH methylation levels in the MR3 region (-1246 to -780) of the MdMYB1 promoter were found to be negatively correlated with MdMYB1 expression. Thus, they were ideal materials to study DNA methylation in apple sports. The protein of RNA-directed DNA methylation (RdDM) pathway responsible for CHH methylation, MdAGO4, was found to interact with the MdMYB1 promoter. MdAGO4s can interact with MdRDM1 and MdDRM2s to form an effector complex, fulfilling CHH methylation. When MdAGO4s and MdDRM2s were overexpressed in apple calli and Arabidopsis mutants, those proteins increase the CHH methylation of AGO4-binding sites. In electrophoretic mobility shift assays, MdAGO4s were found to specifically bind to sequence containing ATATCAGA. Knockdown of MdNRPE1 did not affect the binding of MdAGO4s to the c3 region of the MdMYB1 promoter in 35S::AGO4 calli. Taken together, our data show that the MdMYB1 locus is methylated through binding of MdAGO4s to the MdMYB1 promoter to regulate anthocyanin biosynthesis by the RdDM pathway.
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Affiliation(s)
- Shenghui Jiang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Nan Wang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Min Chen
- Chinese Academy of SciencesYantai Institute of Coastal Zone ResearchYantaiChina
| | | | - Qingguo Sun
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Haifeng Xu
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Zongying Zhang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Yicheng Wang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Xiuqi Sui
- Yantai Modern Fruit Industry Development CompanyYantai Modern Fruit Industry Research InstituteYantaiChina
| | | | - Hongcheng Fang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Weifang Zuo
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Mengyu Su
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Jing Zhang
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Xuesen Chen
- College of Horticulture Science and EngineeringState Key Laboratory of Crop BiologyCollaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in ShandongShandong Agricultural UniversityTai'anChina
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24
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Atighi MR, Verstraeten B, De Meyer T, Kyndt T. Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants. New Phytol 2020; 227:545-558. [PMID: 32162327 PMCID: PMC7317725 DOI: 10.1111/nph.16532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 05/22/2023]
Abstract
A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants.
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Affiliation(s)
| | | | - Tim De Meyer
- Department of Data Analysis & Mathematical ModellingGhent UniversityB‐9000GhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyGhent UniversityB‐9000GhentBelgium
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25
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Xu L, Yuan K, Yuan M, Meng X, Chen M, Wu J, Li J, Qi Y. Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements. Mol Plant 2020; 13:851-863. [PMID: 32087371 DOI: 10.1016/j.molp.2020.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.
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Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kun Yuan
- 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
| | - Meng Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiangbing Meng
- 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
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayang Li
- 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.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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26
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Dalakouras A, Papadopoulou KK. Epigenetic Modifications: An Unexplored Facet of Exogenous RNA Application in Plants. Plants (Basel) 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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Zhou J, Liu L, Li Q, Xu W, Li K, Wang ZW, Sun Q. Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis. Plant J 2020; 101:1185-1197. [PMID: 31647592 DOI: 10.1111/tpj.14584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/06/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Intronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant-specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE ). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that a significant number of intronic heterochromatin-containing genes undergo this mechanism. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.
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Affiliation(s)
- Jincong Zhou
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Liangyu Liu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, College of Life Sciences, Capital Normal University, Beijing, China
| | - Qin Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi-Wei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
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28
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Abstract
Cajal bodies (CBs) are nuclear membraneless bodies composed of proteins and RNA. Although it is known that CBs play a role in RNA metabolism and the formation of functional ribonucleoprotein (RNP) particles, the whole breadth of CB functions is far from being fully elucidated. In this short review, we will summarize and discuss the growing body of evidence pointing to an involvement of this subnuclear compartment in plant-virus interactions.
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Affiliation(s)
- Yi Ding
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China;
- Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 201602, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai 201602, China;
- Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 201602, China
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29
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. Plants (Basel) 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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30
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Přibylová A, Čermák V, Tyč D, Fischer L. Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells. Epigenetics Chromatin 2019; 12:54. [PMID: 31511048 PMCID: PMC6737654 DOI: 10.1186/s13072-019-0299-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/22/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Methylation of cytosines is an evolutionarily conserved epigenetic mark that is essential for the control of chromatin activity in many taxa. It acts mainly repressively, causing transcriptional gene silencing. In plants, de novo DNA methylation is established mainly by RNA-directed DNA-methylation pathway. Even though the protein machinery involved is relatively well-described, the course of the initial phases remains covert. RESULTS We show the first detailed description of de novo DNA-methylation dynamics. Since prevalent plant model systems do not provide the possibility to collect homogenously responding material in time series with short intervals, we developed a convenient system based on tobacco BY-2 cell lines with inducible production of siRNAs (from an RNA hairpin) guiding the methylation machinery to the CaMV 35S promoter controlling GFP reporter. These lines responded very synchronously, and a high level of promoter-specific siRNAs triggered rapid promoter methylation with the first increase observed already 12 h after the induction. The previous presence of CG methylation in the promoter did not affect the methylation dynamics. The individual cytosine contexts reacted differently. CHH methylation peaked at about 80% in 2 days and then declined, whereas CG and CHG methylation needed more time with CHG reaching practically 100% after 10 days. Spreading of methylation was only minimal outside the target region in accordance with the absence of transitive siRNAs. The low and stable proportion of 24-nt siRNAs suggested that Pol IV was not involved in the initial phases. CONCLUSIONS Our results show that de novo DNA methylation is a rapid process initiated practically immediately with the appearance of promoter-specific siRNAs and independently of the prior presence of methylcytosines at the target locus. The methylation was precisely targeted, and its dynamics varied depending on the cytosine sequence context. The progressively increasing methylation resulted in a smooth, gradual inhibition of the promoter activity, which was entirely suppressed in 2 days.
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Affiliation(s)
- Adéla Přibylová
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Vojtěch Čermák
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Dimitrij Tyč
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Charles University, Faculty of Science, 128 44, Prague, Czech Republic.
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31
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Wang B, Liu J, Chu L, Jing X, Wang H, Guo J, Yi B. Exogenous Promoter Triggers APETALA3 Silencing through RNA-Directed DNA Methylation Pathway in Arabidopsis. Int J Mol Sci 2019; 20:ijms20184478. [PMID: 31514282 PMCID: PMC6770043 DOI: 10.3390/ijms20184478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/16/2022] Open
Abstract
The development of floral organs plays a vital role in plant reproduction. In our research, the APETALA3 (AP3) promoter-transgenic lines showed abnormal developmental phenotypes in stamens and petals. The aim of this study is to understand the molecular mechanisms of the morphological defects in transgenic plants. By performing transgenic analysis, it was found that the AP3-promoted genes and the vector had no relation to the morphological defects. Then, we performed the expression analysis of the class A, B, and C genes. A dramatic reduction of transcript levels of class B genes (AP3 and PISTILLATA) was observed. Additionally, we also analyzed the methylation of the promoters of class B genes and found that the promoter of AP3 was hypermethylated. Furthermore, combining mutations in rdr2-2, drm1/2, and nrpd1b-11 with the AP3-silencing lines rescued the abnormal development of stamens and petals. The expression of AP3 was reactivated and the methylation level of AP3 promoter was also reduced in RdDM-defective AP3-silencing lines. Our results showed that the RdDM pathway contributed to the transcriptional silencing in the transgenic AP3-silencing lines. Moreover, the results revealed that fact that the exogenous fragment of a promoter could trigger the methylation of homologous endogenous sequences, which may be ubiquitous in transgenic plants.
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Affiliation(s)
- Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Jing
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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32
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Basso A, Barcaccia G, Galla G. Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions. Plants (Basel) 2019; 8:E158. [PMID: 31181659 PMCID: PMC6631971 DOI: 10.3390/plants8060158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
The protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1-2 were found to be differentially expressed in ovules of apomictic Hypericum perforatum L. accessions. To gain further insight into the expression and regulation of these genes in the context of apomixis, we investigated genomic, transcriptional and functional aspects of the gene family in this species. The H. perforatum genome encodes for two IDN2-like and 7 FDM-like genes. Differential and heterochronic expression of FDM4-like genes was found in H. perforatum pistils. The involvement of these genes in reproduction and seed development is consistent with the observed reduction of the seed set and high variability in seed size in A. thaliana IDN2 and FDM-like knockout lines. Differential expression of IDN2-like and FDM-like genes in H. perforatum was predicted to affect the network of potential interactions between these proteins. Furthermore, pistil transcript levels are modulated by cytokinin and auxin but the effect operated by the two hormones depends on the reproductive phenotype.
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Affiliation(s)
- Andrea Basso
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
| | - Gianni Barcaccia
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
| | - Giulio Galla
- Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell' Università, 1635020 Legnaro, Italy.
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Azevedo J, Picart C, Dureau L, Pontier D, Jaquinod-Kieffer S, Hakimi MA, Lagrange T. UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis. FEBS Open Bio 2019; 9:973-985. [PMID: 30951268 PMCID: PMC6487834 DOI: 10.1002/2211-5463.12627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/21/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022] Open
Abstract
Repeated sequence expression and transposable element mobilization are tightly controlled by multilayer processes, which include DNA 5′‐cytosine methylation. The RNA‐directed DNA methylation (RdDM) pathway, which uses siRNAs to guide sequence‐specific directed DNA methylation, emerged specifically in plants. RdDM ensures DNA methylation maintenance on asymmetric CHH sites and specifically initiates de novo methylation in all cytosine sequence contexts through the action of DRM DNA methyltransferases, of which DRM2 is the most prominent. The RdDM pathway has been well described, but how DRM2 is recruited onto DNA targets and associates with other RdDM factors remains unknown. To address these questions, we developed biochemical approaches to allow the identification of factors that may escape genetic screens, such as proteins encoded by multigenic families. Through both conventional and affinity purification of DRM2, we identified DEAD box RNA helicases U2AF56 Associated Protein 56 (UAP56a/b), which are widespread among eukaryotes, as new DRM2 partners. We have shown that, similar to DRM2 and other RdDM actors, UAP56 has chromatin‐associated protein properties. We confirmed this association both in vitro and in vivo in reproductive tissues. In addition, our experiments also suggest that UAP56 may exhibit differential distribution in cells depending on plant organ. While originally identified for its role in splicing, our study suggests that UAP56 may also have other roles, and our findings allow us to initiate discussion about its potential role in the RdDM pathway.
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Affiliation(s)
- Jacinthe Azevedo
- LGDP-UMR5096, CNRS, Perpignan, France.,LGDP-UMR5096, Université de Perpignan Via Domitia, France
| | - Claire Picart
- LGDP-UMR5096, CNRS, Perpignan, France.,LGDP-UMR5096, Université de Perpignan Via Domitia, France
| | - Laurent Dureau
- LGDP-UMR5096, CNRS, Perpignan, France.,LGDP-UMR5096, Université de Perpignan Via Domitia, France
| | - Dominique Pontier
- LGDP-UMR5096, CNRS, Perpignan, France.,LGDP-UMR5096, Université de Perpignan Via Domitia, France
| | - Sylvie Jaquinod-Kieffer
- Laboratoire Biologie Grande Echelle, Institut de Biosciences et Biotechnologies de Grenoble, UMR_S 1038, CEA, INSERM, Université Grenoble Alpes, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, France
| | - Thierry Lagrange
- LGDP-UMR5096, CNRS, Perpignan, France.,LGDP-UMR5096, Université de Perpignan Via Domitia, France
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Iwasaki M, Hyvärinen L, Piskurewicz U, Lopez-Molina L. Non-canonical RNA-directed DNA methylation participates in maternal and environmental control of seed dormancy. eLife 2019; 8:37434. [PMID: 30910007 PMCID: PMC6435323 DOI: 10.7554/elife.37434] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 03/09/2019] [Indexed: 12/29/2022] Open
Abstract
Seed dormancy is an adaptive trait preventing premature germination out of season. In a previous report (Piskurewicz et al., 2016) we showed that dormancy levels are maternally inherited through the preferential maternal allele expression in the seed endosperm of ALLANTOINASE (ALN), a negative regulator of dormancy. Here we show that suppression of ALN paternal allele expression is imposed by non-canonical RNA-directed DNA methylation (RdDM) of the paternal ALN allele promoter. Dormancy levels are further enhanced by cold during seed development. We show that DNA methylation of the ALN promoter is stimulated by cold in a tissue-specific manner through non-canonical RdDM, involving RDR6 and AGO6. This leads to suppression of ALN expression and further promotion of seed dormancy. Our results suggest that tissue-specific and cold-induced RdDM is superimposed to parental allele imprints to deposit in the seed progeny a transient memory of environmental conditions experienced by the mother plant.
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Affiliation(s)
- Mayumi Iwasaki
- Department of Plant Biology, University of Geneva, Geneva, Switzerland
| | - Lena Hyvärinen
- Department of Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Luis Lopez-Molina
- Department of Plant Biology, University of Geneva, Geneva, Switzerland.,Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Zhong S, Xu Y, Yu C, Zhang X, Li L, Ge H, Ren G, Wang Y, Ma J, Zheng Y, Zheng B. Anaphase-promoting complex/cyclosome regulates RdDM activity by degrading DMS3 in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:3899-908. [PMID: 30760603 DOI: 10.1073/pnas.1816652116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During RNA-directed DNA methylation (RdDM), the DDR complex, composed of DRD1, DMS3, and RDM1, is responsible for recruiting DNA polymerase V (Pol V) to silence transposable elements (TEs) in plants. However, how the DDR complex is regulated remains unexplored. Here, we show that the anaphase-promoting complex/cyclosome (APC/C) regulates the assembly of the DDR complex by targeting DMS3 for degradation. We found that a substantial set of RdDM loci was commonly de-repressed in apc/c and pol v mutants, and that the defects in RdDM activity resulted from up-regulated DMS3 protein levels, which finally caused reduced Pol V recruitment. DMS3 was ubiquitinated by APC/C for degradation in a D box-dependent manner. Competitive binding assays and gel filtration analyses showed that a proper level of DMS3 is critical for the assembly of the DDR complex. Consistent with the importance of the level of DMS3, overaccumulation of DMS3 caused defective RdDM activity, phenocopying the apc/c and dms3 mutants. Moreover, DMS3 is expressed in a cell cycle-dependent manner. Collectively, these findings provide direct evidence as to how the assembly of the DDR complex is regulated and uncover a safeguarding role of APC/C in the regulation of RdDM activity.
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Li J, Wang M, Li Y, Zhang Q, Lindsey K, Daniell H, Jin S, Zhang X. Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process. Plant Biotechnol J 2019; 17:435-450. [PMID: 29999579 PMCID: PMC6335067 DOI: 10.1111/pbi.12988] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/04/2018] [Accepted: 07/10/2018] [Indexed: 05/20/2023]
Abstract
Plant regeneration via somatic embryogenesis is time-consuming and highly genotype-dependent. The plant somatic embryogenesis process provokes many epigenetics changes including DNA methylation and histone modification. Recently, an elite cotton Jin668, with an extremely high regeneration ability, was developed from its maternal inbred Y668 cultivar using a Successive Regeneration Acclimation (SRA) strategy. To reveal the underlying mechanism of SRA, we carried out a genome-wide single-base resolution methylation analysis for nonembryogenic calluses (NECs), ECs, somatic embryos (SEs) during the somatic embryogenesis procedure and the leaves of regenerated offspring plants. Jin668 (R4) regenerated plants were CHH hypomethylated compared with the R0 regenerated plants of SRA process. The increase in CHH methylation from NEC to EC was demonstrated to be associated with the RNA-dependent DNA methylation (RdDM) and the H3K9me2-dependent pathway. Intriguingly, the hypomethylated CHH differentially methylated regions (DMRs) of promoter activated some hormone-related and WUSCHEL-related homeobox genes during the somatic embryogenesis process. Inhibiting DNA methylation using zebularine treatment in NEC increased the number of embryos. Our multi-omics data provide new insights into the dynamics of DNA methylation during the plant tissue culture and regenerated offspring plants. This study also reveals that induced hypomethylation (SRA) may facilitate the higher plant regeneration ability and optimize maternal genetic cultivar.
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Affiliation(s)
- Jianying Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yajun Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | | | - Henry Daniell
- Department of BiochemistrySchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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Abstract
Determining the in situ pattern of protein expression is crucial to accurately establish regulatory function and mode of action of any plant developmental program. Here, we describe two immunolocalization procedures that are consistently used to determine subcellular localization of ARGONAUTE proteins in the ovule of the Brassicaceae. The first is performed in resin-embedded semi-thin sections of developing ovules that can be observed under bright-field microscopy. The second is based in polyacrylamide immersion of complete (whole-mounted) gynoecia or ovules that are observed under confocal microscopy. Both procedures have been successfully performed to localize proteins involved in RNA-directed DNA methylation during the development of the anatropous bitegmic ovule in Arabidopsis, Brassica, or Boechera species.
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Affiliation(s)
- Gloria León-Martínez
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Edgar Demesa-Arévalo
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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Galla G, Basso A, Grisan S, Bellucci M, Pupilli F, Barcaccia G. Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions. Front Plant Sci 2019; 10:654. [PMID: 31178879 PMCID: PMC6543059 DOI: 10.3389/fpls.2019.00654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/01/2019] [Indexed: 05/09/2023]
Abstract
Hypericum perforatum L. (2n = 4x = 32) is an attractive model system for the study of aposporous apomixis. The earliest phenotypic features of aposporous apomixis in this species are the mitotic formation of unreduced embryo sacs from a somatic cell of the ovule nucellus and the avoidance of meiosis. In this research we addressed gene expression variation in sexual and apomictic plants, by focusing on the ovule nucellus, which is the cellular domain primarily involved into the differentiation of meiocyte precursors and aposporous embryo sacs, at a pre-meiotic developmental stage. Gene expression analyses performed by RNAseq identified 396 differentially expressed genes and 1834 transcripts displaying phenotype-specific expression. Furthermore, the sequencing and assembly of the genome from a diploid sexual accession allowed the annotation of a 50 kb sequence portion located upstream the HAPPY locus and to address the extent to which single transcripts were assembled in multiple variants and their co-expression levels. About one third of identified DEGs and phenotype-specific transcripts were associated to transcript variants with alternative expression patterns. Additionally, considering DEGs and phenotype-specific transcript, the co-expression level was estimated in about two transcripts per locus. Our gene expression study shows massive differences in the expression of several genes encoding for transposable elements. Transcriptional differences in the ovule nucellus and pistil terminal developmental stages were also found for subset of genes encoding for potentially interacting proteins involved in pre-mRNA splicing. Furthermore, the sexual and aposporous ovule transcriptomes were characterized by differential expression in genes operating in RNA silencing, RNA-mediated DNA methylation (RdDM) and histone and chromatin modifications. These findings are consistent with a role of these processes in regulating cell fate determination in the ovule, as indicated by forward genetic studies in sexual model species. The association between aposporous apomixis, pre-mRNA splicing and DNA methylation mediated by sRNAs, which is supported by expression data and by the enrichment in GO terms related to these processes, is consistent with the massive differential expression of multiple transposon-related sequences observed in ovules collected from both sexual and aposporous apomictic accessions. Overall, our data suggest that phenotypic expression of aposporous apomixis is concomitant with the modulation of key genes involved in the two interconnected processes: RNA splicing and RNA-directed DNA methylation.
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Affiliation(s)
- Giulio Galla
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
- *Correspondence: Giulio Galla,
| | - Andrea Basso
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
| | - Simone Grisan
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Michele Bellucci
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources, Research Division of Perugia, National Research Council, Perugia, Italy
| | - Gianni Barcaccia
- Laboratory of Genetics and Genomics, Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, University of Padova, Padua, Italy
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Cheng J, Niu Q, Zhang B, Chen K, Yang R, Zhu JK, Zhang Y, Lang Z. Downregulation of RdDM during strawberry fruit ripening. Genome Biol 2018; 19:212. [PMID: 30514401 PMCID: PMC6280534 DOI: 10.1186/s13059-018-1587-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/15/2018] [Indexed: 01/09/2023] Open
Abstract
Background Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during the ripening of non-climacteric fruits are unknown. Results Here, we generate single-base resolution maps of the DNA methylome in immature and ripe strawberry. We observe an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. Application of a DNA methylation inhibitor causes an early ripening phenotype, suggesting that DNA hypomethylation is important for strawberry fruit ripening. The mechanisms underlying DNA hypomethylation during the ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes are not upregulated during the ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation are downregulated during strawberry ripening. Further, ripening-induced DNA hypomethylation is associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that a downregulation of RdDM contributes to DNA hypomethylation during strawberry ripening. Conclusions Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climacteric fruit and suggest a novel function of RdDM in regulating an important process in plant development. Electronic supplementary material The online version of this article (10.1186/s13059-018-1587-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingfeng Niu
- University of the Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Ruihua Yang
- Horticultural Department, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jian-Kang Zhu
- University of the Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhaobo Lang
- University of the Chinese Academy of Sciences, Beijing, 100049, China. .,Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Cambiagno DA, Nota F, Zavallo D, Rius S, Casati P, Asurmendi S, Alvarez ME. Immune receptor genes and pericentromeric transposons as targets of common epigenetic regulatory elements. Plant J 2018; 96:1178-1190. [PMID: 30238536 DOI: 10.1111/tpj.14098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/24/2018] [Accepted: 09/03/2018] [Indexed: 05/04/2023]
Abstract
Pattern recognition receptors (PRR) and nucleotide-binding leucine-rich repeat proteins (NLR) are major components of the plant immune system responsible for pathogen detection. To date, the transcriptional regulation of PRR/NLR genes is poorly understood. Some PRR/NLR genes are affected by epigenetic changes of neighboring transposable elements (TEs) (cis regulation). We analyzed whether these genes can also respond to changes in the epigenetic marks of distal pericentromeric TEs (trans regulation). We found that Arabidopsis tissues infected with Pseudomonas syringae pv. tomato (Pst) initially induced the expression of pericentromeric TEs, and then repressed it by RNA-directed DNA methylation (RdDM). The latter response was accompanied by the accumulation of small RNAs (sRNAs) mapping to the TEs. Curiously these sRNAs also mapped to distal PRR/NLR genes, which were controlled by RdDM but remained induced in the infected tissues. Then, we used non-infected mom1 (Morpheus' molecule 1) mutants that expressed pericentromeric TEs to test if they lose repression of PRR/NLR genes. mom1 plants activated several PRR/NLR genes that were unlinked to MOM1-targeted TEs, and showed enhanced resistance to Pst. Remarkably, the increased defenses of mom1 were abolished when MOM1/RdDM-mediated pericentromeric TEs silencing was re-established. Therefore, common sRNAs could control PRR/NLR genes and distal pericentromeric TEs and preferentially silence TEs when they are activated.
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Affiliation(s)
- Damián A Cambiagno
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Sebastián Rius
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Buenos Aires, Argentina
| | - María E Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Córdoba, Argentina
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Yadav NS, Khadka J, Domb K, Zemach A, Grafi G. CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA. Epigenetics Chromatin 2018; 11:69. [PMID: 30446008 PMCID: PMC6238269 DOI: 10.1186/s13072-018-0240-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting). RESULTS We wanted to explore the regulatory pathway responsible for EK silencing in the Ler ecotype and its effect on CMT1 transcription. Methylome databases confirmed that EK retroelement is heavily methylated and methylation is extended toward CMT1 downstream region. Strong transcriptional activation of EK accompanied by significant reduction in non-CG methylation was found in cmt3 and kyp2, but not in ddm1 or RdDM mutants. EK activation in cmt3 and kyp2 did not interfere with upstream CMT1 expression but abolish transcription through the EK. We identified, in wild-type Ler, three spliced variants in which the entire EK is spliced out; one variant (25% of splicing incidents) facilitates proper reconstitution of an intact CMT1 mRNA. We could recover very low amount of the full-length CMT1 mRNA from WT Ler and Col, but not from cmt3 mutant. CONCLUSIONS Our findings highlight CMT3-SUVH4/KYP as the major pathway silencing the intragenic EK via inducing non-CG methylation. Furthermore, retroelement insertion within exons (e.g., CMT1) may not lead to a complete abolishment of the gene product when the element is kept silent. Rather the element can be spliced out to bring about reconstruction of an intact, functional mRNA and possibly retrieval of an active protein.
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Affiliation(s)
- Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Janardan Khadka
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Katherine Domb
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Assaf Zemach
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel.
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Pérez-González A, Caro E. Effect of transcription terminator usage on the establishment of transgene transcriptional gene silencing. BMC Res Notes 2018; 11:511. [PMID: 30055650 PMCID: PMC6064074 DOI: 10.1186/s13104-018-3649-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
Objective Obtaining high and stable transgene expression is of vital importance for plant genetic engineering. A lot is known about the relationship between terminator efficiency and gene expression, but no studies have addressed the relationship between terminator usage and transgene expression stability or heritable gene silencing. In this paper, we aim to analyze if terminators are a determining factor in the establishment of promoter DNA methylation of plant transgenes. Results Our experiments comparing plants with a LUC reporter under the 35S CaMV promoter and good efficiency terminators (Thsp, T35S) show that the use of efficient terminator sequences does not avoid the accumulation of promoter DNA methylation and transgene silencing. However, Thsp lead to a higher reporter gene expression and lower promoter DNA methylation levels than T35S, supporting that terminator usage is indeed involved in the establishment of TGS by methylation of transgenes’ promoters. In the case of a terminatorless construct, the PTGS initiated by the improperly terminated mRNAs is not followed by the establishment of heritable silencing in the form of strong promoter DNA methylation, like in the case of TAS genes and reactivated TEs (for the transgene DNA methylation levels remained below the 20%). Electronic supplementary material The online version of this article (10.1186/s13104-018-3649-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Pérez-González
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, 28223, Madrid, Spain.
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Duan CG, Zhu JK. Dissecting the Subnuclear Localization Patterns of Argonaute Proteins and Other Components of the RNA-Directed DNA Methylation Pathway in Plants. Methods Mol Biol 2017; 1640:129-35. [PMID: 28608338 DOI: 10.1007/978-1-4939-7165-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA-directed DNA methylation (RdDM) is a nuclear pathway which is comprised of multiple main and accessory protein components, including two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V, and argonaute (AGO) proteins. Regulation in the RdDM pathway can be achieved via multiple mechanisms, including the spatial distribution of different RdDM components. Here we describe a protocol for dissecting the subnuclear localization of AGO proteins and other RdDM components, including nuclei extraction from seedlings, slide preparation, and subsequent immunostaining.
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McKinlay A, Podicheti R, Wendte JM, Cocklin R, Rusch DB. RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis. RNA Biol 2017; 15:269-279. [PMID: 29199514 DOI: 10.1080/15476286.2017.1409930] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3' boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.
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Affiliation(s)
- Anastasia McKinlay
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ram Podicheti
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA.,c School of Informatics and Computing, Indiana University , Bloomington , IN , USA
| | - Jered M Wendte
- a Department of Biology , Indiana University , Bloomington , Indiana , USA
| | - Ross Cocklin
- a Department of Biology , Indiana University , Bloomington , Indiana , USA.,d Howard Hughes Medical Institute, Indiana University , Bloomington , Indiana
| | - Douglas B Rusch
- b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA
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Forestan C, Farinati S, Aiese Cigliano R, Lunardon A, Sanseverino W, Varotto S. Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription. BMC Plant Biol 2017; 17:161. [PMID: 29025411 PMCID: PMC5639751 DOI: 10.1186/s12870-017-1108-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/04/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles. RESULTS In this study we applied a total RNA-Seq approach to compare the B73 and rpd1/rmr6 leaf transcriptomes. Although previous studies indicated that loss of siRNAs production in RdDM mutants provokes a strong loss of CHH DNA methylation but not massive gene or TEs transcriptional activation in both Arabidopsis and maize, our total RNA-Seq analysis of rpd1/rmr6 transcriptome reveals that loss of Pol IV activity causes a global increase in the transcribed fraction of the maize genome. Our results point to the genes with nearby TE insertions as being the most strongly affected by Pol IV-mediated gene silencing. TEs modulation of nearby gene expression is linked to alternative methylation profiles on gene flanking regions, and these profiles are strictly dependent on specific characteristics of the TE member inserted. Although Pol IV is essential for the biogenesis of siRNAs, the genes with associated siRNA loci are less affected by the pol IV mutation. CONCLUSIONS This deep and integrated analysis of gene expression, TEs distribution, smallRNA targeting and DNA methylation levels, reveals that loss of Pol IV activity globally affects genome regulation, pointing at TEs as modulator of nearby gene expression and indicating the existence of multiple level epigenetic silencing mechanisms. Our results also suggest a predominant role of the Pol IV-mediated RdDM pathway in genome dominance regulation, and subgenome stability and evolution in maize.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | - Silvia Farinati
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | | | - Alice Lunardon
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, PA 16802 USA
| | | | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
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Bouyer D, Kramdi A, Kassam M, Heese M, Schnittger A, Roudier F, Colot V. DNA methylation dynamics during early plant life. Genome Biol 2017; 18:179. [PMID: 28942733 PMCID: PMC5611644 DOI: 10.1186/s13059-017-1313-0] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022] Open
Abstract
Background Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. Results Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10–20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Conclusion Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1313-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Bouyer
- Institut de Biologie Moléculaire des Plantes du CNRS - UPR2357, Université de Strasbourg, Strasbourg, France. .,Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, F-75230, Paris, France.
| | - Amira Kramdi
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, F-75230, Paris, France
| | - Mohamed Kassam
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, F-75230, Paris, France.,Present address: Nestlé Institute of Health Sciences, Functional Genomics, Lausanne, Switzerland
| | - Maren Heese
- Institut de Biologie Moléculaire des Plantes du CNRS - UPR2357, Université de Strasbourg, Strasbourg, France.,Department of Developmental Biology, University of Hamburg, Biozentrum Klein Flottbek, Hamburg, Germany
| | - Arp Schnittger
- Institut de Biologie Moléculaire des Plantes du CNRS - UPR2357, Université de Strasbourg, Strasbourg, France.,Department of Developmental Biology, University of Hamburg, Biozentrum Klein Flottbek, Hamburg, Germany
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, F-75230, Paris, France.,Present address: Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, F-75230, Paris, France
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You C, Cui J, Wang H, Qi X, Kuo LY, Ma H, Gao L, Mo B, Chen X. Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biol 2017; 18:158. [PMID: 28835265 PMCID: PMC5569507 DOI: 10.1186/s13059-017-1291-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants. Results Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms. Conclusions Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1291-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China
| | - Hui Wang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, People's Republic of China
| | - Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China.
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China. .,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA. .,Howard Hughes Medical Institute, University of California, Riverside, 92521, CA, USA.
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Guo X, Ma Z, Zhang Z, Cheng L, Zhang X, Li T. Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple. Front Plant Sci 2017; 8:873. [PMID: 28611800 PMCID: PMC5447065 DOI: 10.3389/fpls.2017.00873] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 05/10/2017] [Indexed: 05/22/2023]
Abstract
Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined. Here, we performed Illumina sequencing of sRNA libraries prepared from vegetative and floral bud during flower induction of the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and six novel members display significant differential expression (DE) patterns. Notably, most of these DE-miRNAs in floral transition displayed opposite expression changes in reported phase transition in apple trees. Bioinformatics analysis suggests most of the DE-miRNAs targeted transcripts involved in SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene regulation, stress responses, and auxin and gibberellin (GA) pathways, with further suggestion that there is an inherent link between physiological stress response and metabolism reprogramming during floral transition. We also observed significant changes in 24 nucleotide (nt) sRNAs that are hallmarks for RNA-dependent DNA methylation (RdDM) pathway, suggestive of the correlation between epigenetic modifications and the floral transition. The study not only provides new insight into our understanding of fundamental mechanism of poorly studied floral transition in apple and other woody plants, but also presents important sRNA resource for future in-depth research in the apple flowering physiology.
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Affiliation(s)
- Xinwei Guo
- Department of Fruit Science, College of Horticulture, China Agricultural UniversityBeijing, China
- Department of Biochemistry and Biophysics, Texas A&M UniversityCollege Station, TX, United States
- Institute for Plant Genomics and Biotechnology, Texas A&M UniversityCollege Station, TX, United States
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M UniversityCollege Station, TX, United States
- Institute for Plant Genomics and Biotechnology, Texas A&M UniversityCollege Station, TX, United States
| | - Zhonghui Zhang
- Department of Biochemistry and Biophysics, Texas A&M UniversityCollege Station, TX, United States
- Institute for Plant Genomics and Biotechnology, Texas A&M UniversityCollege Station, TX, United States
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal UniversityGuangzhou, China
| | - Lailiang Cheng
- Department of Horticulture, Cornell UniversityIthaca, NY, United States
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M UniversityCollege Station, TX, United States
- Institute for Plant Genomics and Biotechnology, Texas A&M UniversityCollege Station, TX, United States
- *Correspondence: Xiuren Zhang
| | - Tianhong Li
- Department of Fruit Science, College of Horticulture, China Agricultural UniversityBeijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit TreesBeijing, China
- Tianhong Li
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Lahmy S, Pontier D, Bies-Etheve N, Laudié M, Feng S, Jobet E, Hale CJ, Cooke R, Hakimi MA, Angelov D, Jacobsen SE, Lagrange T. Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes Dev 2016; 30:2565-2570. [PMID: 27986858 PMCID: PMC5204349 DOI: 10.1101/gad.289553.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/17/2016] [Indexed: 12/29/2022]
Abstract
RNA polymerase V (Pol V) long noncoding RNAs (lncRNAs) have been proposed to guide ARGONAUTE4 (AGO4) to chromatin in RNA-directed DNA methylation (RdDM) in plants. Here, we provide evidence, based on laser UV-assisted zero-length cross-linking, for functionally relevant AGO4-DNA interaction at RdDM targets. We further demonstrate that Pol V lncRNAs or the act of their transcription are required to lock Pol V holoenzyme into a stable DNA-bound state that allows AGO4 recruitment via redundant glycine-tryptophan/tryptophan-glycine AGO hook motifs present on both Pol V and its associated factor, SPT5L. We propose a model in which AGO4-DNA interaction could be responsible for the unique specificities of RdDM.
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Affiliation(s)
- Sylvie Lahmy
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Michèle Laudié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Suhua Feng
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Christopher J Hale
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Pathology, Center for Precision Diagnostics, University of Washington, Seattle, Washington 98195, USA
| | - Richard Cooke
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), UMR5309, CNRS, U1209, Institut National de la Santé et de la Recherche Médicale (INSERM), Grenoble Alpes University, 38000 Grenoble, France
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule (LBMC), UMR 5239, CNRS/École Normale Supérieure de Lyon (ENSL)/Université Claude Bernard Lyon 1 (UCBL), 69007 Lyon, France.,Institut NeuroMyogène (INMG), UMR 5310, CNRS/UCBL/ENSL, 69007 Lyon, France
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes (LGDP), UMR5096, Centre National de la Recherche Scientifique (CNRS), Université de Perpignan via Domitia (UPVD), 66860 Perpignan, France
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50
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Hamera S, Yan Y, Song X, Chaudhary SU, Murtaza I, Su L, Tariq M, Chen X, Fang R. Expression of Cucumber mosaic virus suppressor 2b alters FWA methylation and its siRNA accumulation in Arabidopsis thaliana. Biol Open 2016; 5:1727-1734. [PMID: 27659688 PMCID: PMC5155521 DOI: 10.1242/bio.017244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Cucumber mosaic virus (CMV) suppressor 2b co-localizes with AGO4 in cytoplasmic and nuclear fractions of Arabidopsis thaliana Biochemical fractionation of A. thaliana cellular extracts revealed that 2b and AGO4 coexist in multiple size exclusions. 2b transgenic A. thaliana exhibited an enhanced accumulation of 24nt siRNAs from flowering wageningen (FWA) and other heterochromatic loci. These plants also exhibited hypo-methylation of an endogenous- as well as transgene-FWA promoter at non-CG sites. In corroboration, both transgenic 2b and CMV infection affected the regulation of transposons which mimics the ago4 phenotype. In conclusion, 2b perturbs plant defense by interfering with AGO4-regulated transcriptional gene silencing.
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Affiliation(s)
- Sadia Hamera
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan .,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Youngsheng Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoguang Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Safee Ullah Chaudhary
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
| | - Iram Murtaza
- Department of Biochemistry, Quaid i Azam University, Islamabad 54320, Pakistan
| | - Lei Su
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Muhammad Tariq
- SBA School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore 54792, Pakistan
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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