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Yue Z, Deng C, Zeng Y, Shang H, Wang S, Liu S, Liu H. Phyllostachys edulis argonaute genes function in the shoot architecture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 345:112114. [PMID: 38735397 DOI: 10.1016/j.plantsci.2024.112114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/29/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Argonaute (AGO) proteins are the core components of the RNA-induced silencing complexes (RISC) in the cytoplasm and nucleus, and are necessary for the development of plant shoot meristem, which gives rise to the above-ground plant body. In this study, we identified 23 Phyllostachys edulis AGO genes (PhAGOs) that were distributed unequally on the 14 unmapped scaffolds. Gene collinearity and phylogeny analysis showed that the innovation of PhAGO genes was mainly due to dispersed duplication and whole-genome duplication, which resulted in the enlarged PhAGO family. PhAGO genes were expressed in a temporal-spatial expression pattern, and they encoded proteins differently localized in the cytoplasm and/or nucleus. Overexpression of the PhAGO2 and PhAGO4 genes increased the number of tillers or leaves in Oryza sativa and affected the shoot architecture of Arabidopsis thaliana. These results provided insight into the fact that PhAGO genes play important roles in plant development.
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Affiliation(s)
- Zhiqiang Yue
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China
| | - Chu Deng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China
| | - Yuxue Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China
| | - Hongna Shang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China.
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, China.
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2
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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2024; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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3
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Takei T, Tsukada M, Tamura K, Hara-Nishimura I, Fukao Y, Kurihara Y, Matsui M, Saze H, Tsuzuki M, Watanabe Y, Hamada T. ARGONAUTE1-binding Tudor domain proteins function in small interfering RNA production for RNA-directed DNA methylation. PLANT PHYSIOLOGY 2024; 195:1333-1346. [PMID: 38446745 DOI: 10.1093/plphys/kiae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Transposable elements (TEs) contribute to plant evolution, development, and adaptation to environmental changes, but the regulatory mechanisms are largely unknown. RNA-directed DNA methylation (RdDM) is 1 TE regulatory mechanism in plants. Here, we identified that novel ARGONAUTE 1 (AGO1)-binding Tudor domain proteins Precocious dissociation of sisters C/E (PDS5C/E) are involved in 24-nt siRNA production to establish RdDM on TEs in Arabidopsis thaliana. PDS5 family proteins are subunits of the eukaryote-conserved cohesin complex. However, the double mutant lacking angiosperm-specific subfamily PDS5C and PDS5E (pds5c/e) exhibited different developmental phenotypes and transcriptome compared with those of the double mutant lacking eukaryote-conserved subfamily PDS5A and PDS5B (pds5a/b), suggesting that the angiosperm-specific PDS5C/E subfamily has a unique function in angiosperm plants. Proteome and imaging analyses revealed that PDS5C/E interact with AGO1. The pds5c/e double mutant had defects in 24-nt siRNA accumulation and CHH DNA methylation on TEs. In addition, some lncRNAs that accumulated in the pds5c/e mutant were targeted by AGO1-loading 21-nt miRNAs and 21-nt siRNAs. These results indicate that PDS5C/E and AGO1 participate in 24-nt siRNA production for RdDM in the cytoplasm. These findings indicate that angiosperm plants evolved a new regulator, the PDS5C/E subfamily, to control the increase in TEs during angiosperm evolution.
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Affiliation(s)
- Takahito Takei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Michio Tsukada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Kentaro Tamura
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | | | - Yoichiro Fukao
- Graduate School of Life Science, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukio Kurihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Department of Life and Environmental System Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Masayuki Tsuzuki
- Faculty of Agriculture and Marine Science, Kochi University, Kochi 783-8502, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takahiro Hamada
- Department of Bioscience, Faculty of Life Science, Okayama University of Science, Okayama 700-0005, Japan
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Harris CJ, Zhong Z, Ichino L, Feng S, Jacobsen SE. H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment. eLife 2024; 12:RP89353. [PMID: 38814684 PMCID: PMC11139477 DOI: 10.7554/elife.89353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT DNA methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in an h1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase, Pol V. Loss of H1 resulted in NRPE1 enrichment predominantly in heterochromatic TEs. Increased NRPE1 binding was associated with increased chromatin accessibility in h1, suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 corresponded to the loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 similarly restricts the occupancy of the methylation reader, SUVH1, and polycomb-mediated H3K27me3. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.
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Affiliation(s)
- C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Lucia Ichino
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
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Liu Y, Shu J, Zhang Z, Ding N, Liu J, Liu J, Cui Y, Wang C, Chen C. A conserved Pol II elongator SPT6L mediates Pol V transcription to regulate RNA-directed DNA methylation in Arabidopsis. Nat Commun 2024; 15:4460. [PMID: 38796517 PMCID: PMC11127964 DOI: 10.1038/s41467-024-48940-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNAs and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components have been uncovered that are involved in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we report that the conserved RNA polymerase II (Pol II) elongator, SPT6L, binds to thousands of intergenic regions in a Pol II-independent manner. The intergenic enrichment of SPT6L, interestingly, co-occupies with the largest subunit of Pol V (NRPE1) and mutation of SPT6L leads to the reduction of DNA methylation but not Pol V enrichment. Furthermore, the association of SPT6L at Pol V loci is dependent on the Pol V associated factor, SPT5L, rather than the presence of Pol V, and the interaction between SPT6L and NRPE1 is compromised in spt5l. Finally, Pol V RIP-seq reveals that SPT6L is required to maintain the amount and length of Pol V transcripts. Our findings thus uncover the critical role of a Pol II conserved elongator in Pol V mediated DNA methylation and transcription, and shed light on the mutual regulation between Pol V and II in plants.
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Affiliation(s)
- Yujuan Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Shu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zhi Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Ding
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jinyuan Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Liu
- Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
- Department of Biology, Western University, London, ON, N6A 5B7, Canada
| | - Changhu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chen Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Imaduwage I, Hewadikaram M. Predicted roles of long non-coding RNAs in abiotic stress tolerance responses of plants. MOLECULAR HORTICULTURE 2024; 4:20. [PMID: 38745264 PMCID: PMC11094901 DOI: 10.1186/s43897-024-00094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/06/2024] [Indexed: 05/16/2024]
Abstract
The plant genome exhibits a significant amount of transcriptional activity, with most of the resulting transcripts lacking protein-coding potential. Non-coding RNAs play a pivotal role in the development and regulatory processes in plants. Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides, may play a significant role in enhancing plant resilience to various abiotic stresses, such as excessive heat, drought, cold, and salinity. In addition, the exogenous application of chemicals, such as abscisic acid and salicylic acid, can augment plant defense responses against abiotic stress. While how lncRNAs play a role in abiotic stress tolerance is relatively well-studied in model plants, this review provides a comprehensive overview of the current understanding of this function in horticultural crop plants. It also delves into the potential role of lncRNAs in chemical priming of plants in order to acquire abiotic stress tolerance, although many limitations exist in proving lncRNA functionality under such conditions.
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Affiliation(s)
- Iuh Imaduwage
- Department of Biomedical Sciences, Faculty of Science, NSBM Green University, Pitipana, Homagama, Sri Lanka
| | - Madhavi Hewadikaram
- Department of Biomedical Sciences, Faculty of Science, NSBM Green University, Pitipana, Homagama, Sri Lanka.
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7
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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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8
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Iwakawa HO. The clade-specific target recognition mechanisms of plant RISCs. Nucleic Acids Res 2024:gkae257. [PMID: 38621714 DOI: 10.1093/nar/gkae257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Eukaryotic Argonaut proteins (AGOs) assemble RNA-induced silencing complexes (RISCs) with guide RNAs that allow binding to complementary RNA sequences and subsequent silencing of target genes. The model plant Arabidopsis thaliana encodes 10 different AGOs, categorized into three distinct clades based on amino acid sequence similarity. While clade 1 and 2 RISCs are known for their roles in post-transcriptional gene silencing, and clade 3 RISCs are associated with transcriptional gene silencing in the nucleus, the specific mechanisms of how RISCs from each clade recognize their targets remain unclear. In this study, I conducted quantitative binding analyses between RISCs and target nucleic acids with mismatches at various positions, unveiling distinct target binding characteristics unique to each clade. Clade 1 and 2 RISCs require base pairing not only in the seed region but also in the 3' supplementary region for stable target RNA binding, with clade 1 exhibiting a higher stringency. Conversely, clade 3 RISCs tolerate dinucleotide mismatches beyond the seed region. Strikingly, they bind to DNA targets with an affinity equal to or surpassing that of RNA, like prokaryotic AGO complexes. These insights challenge existing views on plant RNA silencing and open avenues for exploring new functions of eukaryotic AGOs.
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Affiliation(s)
- Hiro-Oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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9
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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, MD.) 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] [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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10
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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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11
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McEvoy SL, Grady PGS, Pauloski N, O'Neill RJ, Wegrzyn JL. Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology. Evol Appl 2024; 17:e13669. [PMID: 38633133 PMCID: PMC11022628 DOI: 10.1111/eva.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 04/19/2024] Open
Abstract
DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.
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Affiliation(s)
- Susan L. McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Department of Forest SciencesUniversity of HelsinkiHelsinkiFinland
| | - Patrick G. S. Grady
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Nicole Pauloski
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Rachel J. O'Neill
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsConnecticutUSA
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12
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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13
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Dew-Budd KJ, Chow HT, Kendall T, David BC, Rozelle JA, Mosher RA, Beilstein MA. Mating system is associated with seed phenotypes upon loss of RNA-directed DNA methylation in Brassicaceae. PLANT PHYSIOLOGY 2024; 194:2136-2148. [PMID: 37987565 DOI: 10.1093/plphys/kiad622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 11/22/2023]
Abstract
In plants, de novo DNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes in Arabidopsis (Arabidopsis thaliana), where the pathway has been most thoroughly studied. In contrast, Brassica rapa mutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in 3 additional members of the Brassicaceae family: Camelina sativa, Capsella rubella, and Capsella grandiflora. Among these 3 species, only mutations in the obligate outcrosser, C. grandiflora, displayed a seed production defect similar to Brassica rapa mutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
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Affiliation(s)
- Kelly J Dew-Budd
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Hiu Tung Chow
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Timmy Kendall
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Brandon C David
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - James A Rozelle
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rebecca A Mosher
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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14
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation. PLANT PHYSIOLOGY 2024; 194:2511-2532. [PMID: 38109503 PMCID: PMC10980416 DOI: 10.1093/plphys/kiad668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (Mediator of paramutation1), with that of their parents, wild-type siblings, and backcrossed progeny in maize (Zea mays). Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of these DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that both TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in most TCM DMRs in F1 plants required Mop1, initiation of a new epigenetic state of these DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is independent of RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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15
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Zaheer U, Munir F, Salum YM, He W. Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review. PeerJ 2024; 12:e17115. [PMID: 38560454 PMCID: PMC10979746 DOI: 10.7717/peerj.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.
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Affiliation(s)
- Uroosa Zaheer
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Faisal Munir
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yussuf Mohamed Salum
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiyi He
- Plant Protection, State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Plant Protection, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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16
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Zavallo D, Cara N, Leone M, Crescente JM, Marfil C, Masuelli R, Asurmendi S. Assessing small RNA profiles in potato diploid hybrid and its resynthesized allopolyploid reveals conserved abundance with distinct genomic distribution. PLANT CELL REPORTS 2024; 43:85. [PMID: 38453711 DOI: 10.1007/s00299-024-03170-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
KEY MESSAGE The shock produced by the allopolyploidization process on a potato interspecific diploid hybrid displays a non-random remobilization of the small RNAs profile on a variety of genomic features. Allopolyploidy, a complex process involving interspecific hybridization and whole genome duplication, significantly impacts plant evolution, leading to the emergence of novel phenotypes. Polyploids often present phenotypic nuances that enhance adaptability, enabling them to compete better and occasionally to colonize new habitats. Whole-genome duplication represents a genomic "shock" that can trigger genetic and epigenetic changes that yield novel expression patterns. In this work, we investigate the polyploidization effect on a diploid interspecific hybrid obtained through the cross between the cultivated potato Solanum tuberosum and the wild potato Solanum kurtzianum, by assessing the small RNAs (sRNAs) profile of the parental diploid hybrid and its derived allopolyploid. Small RNAs are key components of the epigenetic mechanisms involved in silencing by RNA-directed DNA Methylation (RdDM). A sRNA sequencing (sRNA-Seq) analysis was performed to individually profile the 21 to 22 nucleotide (21 to 22-nt) and 24-nt sRNA size classes due to their unique mechanism of biogenesis and mode of function. The composition and distribution of different genomic features and differentially accumulated (DA) sRNAs were evaluated throughout the potato genome. We selected a subset of genes associated with DA sRNAs for messenger RNA (mRNA) expression analysis to assess potential impacts on the transcriptome. Interestingly, we noted that 24-nt DA sRNAs that exclusively mapped to exons were correlated with differentially expressed mRNAs between genotypes, while this behavior was not observed when 24-nt DA sRNAs were mapped to intronic regions. These findings collectively emphasize the nonstochastic nature of sRNA remobilization in response to the genomic shock induced by allopolyploidization.
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Affiliation(s)
- Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina
| | - Nicolas Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Melisa Leone
- Universidad Nacional de Hurlingham, Instituto de Biotecnología, Av. Vergara 2222 (B1688GEZ), Villa Tesei, Buenos Aires, Argentina
| | - Juan Manuel Crescente
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
| | - Carlos Marfil
- Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria (EEA-Mendoza-INTA), San Martín 3853, Luján de Cuyo, 5534, Mendoza, Argentina
| | - Ricardo Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA - Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Los Reseros y Nicolás Repetto, 1686, Hurlingham, CP, Argentina.
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17
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Harris CJ, Zhong Z, Ichino L, Feng S, Jacobsen SE. H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.539968. [PMID: 37214879 PMCID: PMC10197610 DOI: 10.1101/2023.05.10.539968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT DNA methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in an h1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase, Pol V. Loss of H1 resulted in NRPE1 enrichment predominantly in heterochromatic TEs. Increased NRPE1 binding was associated with increased chromatin accessibility in h1 , suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 corresponded to loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 similarly restricts the occupancy of the methylation reader, SUVH1, and polycomb-mediated H3K27me3. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.
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18
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Corrêa RL, Kutnjak D, Ambrós S, Bustos M, Elena SF. Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistance. BMC PLANT BIOLOGY 2024; 24:172. [PMID: 38443837 PMCID: PMC10913459 DOI: 10.1186/s12870-024-04866-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Plant responses to a wide range of stresses are known to be regulated by epigenetic mechanisms. Pathogen-related investigations, particularly against RNA viruses, are however scarce. It has been demonstrated that Arabidopsis thaliana plants defective in some members of the RNA-directed DNA methylation (RdDM) or histone modification pathways presented differential susceptibility to the turnip mosaic virus. In order to identify genes directly targeted by the RdDM-related RNA Polymerase V (POLV) complex and the histone demethylase protein JUMONJI14 (JMJ14) during infection, the transcriptomes of infected mutant and control plants were obtained and integrated with available chromatin occupancy data for various epigenetic proteins and marks. RESULTS A comprehensive list of virus-responsive gene candidates to be regulated by the two proteins was obtained. Twelve genes were selected for further characterization, confirming their dynamic regulation during the course of infection. Several epigenetic marks on their promoter sequences were found using in silico data, raising confidence that the identified genes are actually regulated by epigenetic mechanisms. The altered expression of six of these genes in mutants of the methyltransferase gene CURLY LEAF and the histone deacetylase gene HISTONE DEACETYLASE 19 suggests that some virus-responsive genes may be regulated by multiple coordinated epigenetic complexes. A temporally separated multiple plant virus infection experiment in which plants were transiently infected with one virus and then infected by a second one was designed to investigate the possible roles of the identified POLV- and JMJ14-regulated genes in wild-type (WT) plants. Plants that had previously been stimulated with viruses were found to be more resistant to subsequent virus challenge than control plants. Several POLV- and JMJ14-regulated genes were found to be regulated in virus induced resistance in WT plants, with some of them poisoned to be expressed in early infection stages. CONCLUSIONS A set of confident candidate genes directly regulated by the POLV and JMJ14 proteins during virus infection was identified, with indications that some of them may be regulated by multiple epigenetic modules. A subset of these genes may also play a role in the tolerance of WT plants to repeated, intermittent virus infections.
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Affiliation(s)
- Régis L Corrêa
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain.
- Department of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, 21941-590, Brazil.
| | - Denis Kutnjak
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Silvia Ambrós
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
| | - Mónica Bustos
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
| | - Santiago F Elena
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Cientificas (CSIC) - Universitat de València (UV), Paterna, Valencia, 46980, Spain
- The Santa Fe Institute, Santa Fe, NM, 87501, USA
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19
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Meca E, Díez CM, Gaut BS. Modeling transposable elements dynamics during polyploidization in plants. J Theor Biol 2024; 579:111701. [PMID: 38128754 DOI: 10.1016/j.jtbi.2023.111701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/24/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
In this work we study the proliferation of transposable elements (TEs) and the epigenetic response of plants during the process of polyploidization. Through a deterministic model, expanding on our previous work on TE proliferation under epigenetic regulation, we study the long-term TE distribution and TE stability in the subgenomes of both autopolyploids and allopolyploids. We also explore different small-interfering RNA (siRNA) action modes on the subgenomes, including a model where siRNAs are not directed to specific genomes and one where siRNAs are directed - i.e. more active - in subgenomes with higher TE loads. In the autopolyploid case, we find long-term stable equilbria that tend to equilibrate the number of active TEs between subgenomes. In the allopolyploid case, directed siRNA action is fundamental to avoid a "winner takes all" outcome of the competition between the TEs in the different subgenomes. We also show that decaying oscillations in the number of TEs occur naturally in all cases, perhaps explaining some of the observed features of 'genomic shock' after hybridization events, and that the balance in the dynamics of the different types of siRNA is determinant for the synchronization of these oscillations.
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Affiliation(s)
- Esteban Meca
- Departamento de Física Aplicada, Radiología y Medicina Física, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Albert Einstein (C2), 14014 Córdoba, Spain.
| | - Concepción M Díez
- Departamento de Agronomía, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio Celestino Mutis (C4), 14014 Córdoba, Spain.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-3875, United States of America.
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20
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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. CELL GENOMICS 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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21
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Venios X, Gkizi D, Nisiotou A, Korkas E, Tjamos SE, Zamioudis C, Banilas G. Emerging Roles of Epigenetics in Grapevine and Winegrowing. PLANTS (BASEL, SWITZERLAND) 2024; 13:515. [PMID: 38498480 PMCID: PMC10893341 DOI: 10.3390/plants13040515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Epigenetics refers to dynamic chemical modifications to the genome that can perpetuate gene activity without changes in the DNA sequence. Epigenetic mechanisms play important roles in growth and development. They may also drive plant adaptation to adverse environmental conditions by buffering environmental variation. Grapevine is an important perennial fruit crop cultivated worldwide, but mostly in temperate zones with hot and dry summers. The decrease in rainfall and the rise in temperature due to climate change, along with the expansion of pests and diseases, constitute serious threats to the sustainability of winegrowing. Ongoing research shows that epigenetic modifications are key regulators of important grapevine developmental processes, including berry growth and ripening. Variations in epigenetic modifications driven by genotype-environment interplay may also lead to novel phenotypes in response to environmental cues, a phenomenon called phenotypic plasticity. Here, we summarize the recent advances in the emerging field of grapevine epigenetics. We primarily highlight the impact of epigenetics to grapevine stress responses and acquisition of stress tolerance. We further discuss how epigenetics may affect winegrowing and also shape the quality of wine.
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Affiliation(s)
- Xenophon Venios
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Danai Gkizi
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Aspasia Nisiotou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “Demeter”, Sofokli Venizelou 1, 14123 Lykovryssi, Greece;
| | - Elias Korkas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
| | - Sotirios E. Tjamos
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos Str., 11855 Athens, Greece;
| | - Christos Zamioudis
- Department of Agricultural Development, Democritus University of Thrace, Pantazidou 193, 68200 Orestiada, Greece;
| | - Georgios Banilas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (D.G.); (E.K.)
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22
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Niu X, Ge Z, Ito H. Regulatory mechanism of heat-active retrotransposons by the SET domain protein SUVH2. FRONTIERS IN PLANT SCIENCE 2024; 15:1355626. [PMID: 38390294 PMCID: PMC10883384 DOI: 10.3389/fpls.2024.1355626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
New transposon insertions are deleterious to genome stability. The RNA-directed DNA methylation (RdDM) pathway evolved to regulate transposon activity via DNA methylation. However, current studies have not yet clearly described the transposition regulation. ONSEN is a heat-activated retrotransposon that is activated at 37°C. The plant-specific SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG (SUVH) family proteins function downstream of the RdDM pathway. The SUVH protein families are linked to TE silencing by two pathways, one through DNA methylation and the other through chromatin remodeling. In this study, we analyzed the regulation of ONSEN activity by SUVH2. We observed that ONSEN transcripts were increased; however, there was no transpositional activity in Arabidopsis suvh2 mutant. The suvh2 mutant produced siRNAs from the ONSEN locus under heat stress, suggesting that siRNAs are involved in suppressing transposition. These results provide new insights into the regulatory mechanisms of retrotransposons that involve siRNA in the RdDM pathway.
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Affiliation(s)
- Xiaoying Niu
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Zhiyu Ge
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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23
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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24
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Contreras-Garrido A, Galanti D, Movilli A, Becker C, Bossdorf O, Drost HG, Weigel D. Transposon dynamics in the emerging oilseed crop Thlaspi arvense. PLoS Genet 2024; 20:e1011141. [PMID: 38295109 PMCID: PMC10881000 DOI: 10.1371/journal.pgen.1011141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/21/2024] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms might contribute to the broad geographic success and adaptive capacity of the emerging oil crop Thlaspi arvense (field pennycress). We classified the TE inventory based on a high-quality genome assembly, estimated the age of retrotransposon TE families and comprehensively assessed their mobilization potential. A survey of 280 accessions from 12 regions across the Northern hemisphere allowed us to quantify over 90,000 TE insertion polymorphisms (TIPs). Their distribution mirrored the genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for transcriptome divergence. The number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation, including an apparent knockout mutation in BROMODOMAIN AND ATPase DOMAIN-CONTAINING PROTEIN 1 (BRAT1), while DNA transposons are associated with variation at the HSP19 heat shock protein gene. We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.
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Affiliation(s)
| | - Dario Galanti
- Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany
| | - Andrea Movilli
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Claude Becker
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Max Planck Institute for Biology Tübingen,Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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25
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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26
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Andreescu M. Epigenetic Alterations That Are the Backbone of Immune Evasion in T-cell Malignancies. Cureus 2024; 16:e51662. [PMID: 38179322 PMCID: PMC10766007 DOI: 10.7759/cureus.51662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 01/06/2024] Open
Abstract
Epigenetic alterations are heritable and enduring modifications in gene expression that play a pivotal role in immune evasion. These include alterations to noncoding RNA, DNA methylation, and histone modifications. DNA methylation plays a crucial role in normal cell growth and development but alterations in methylation patterns such as hypermethylation or hypomethylation can enable tumor and viral cells to evade host immune responses. Histone modifications can also inhibit immune responses by promoting the expression of genes involved in suppressing normal immune function. In the case of T-cell lymphoma, adult T-cell lymphomas (ATL) also undergo immune evasion through the exceptional function of its accessory and regulatory genes. Epigenetic therapies are emerging as a promising adjunct to traditional immunotherapy and chemotherapy regimens. Clinical trials are currently investigating the use of epigenetic therapies in combination with immunotherapies and chemotherapies for more effective treatment of ATL and other cancers. This review highlights epigenetic alterations that are widely found in T-cell malignancies.
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27
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de Tomás C, Vicient CM. The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants. EPIGENOMES 2023; 8:2. [PMID: 38247729 PMCID: PMC10801548 DOI: 10.3390/epigenomes8010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.
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Affiliation(s)
| | - Carlos M. Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
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28
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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29
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Tselika M, Belmezos N, Kallemi P, Andronis C, Chiumenti M, Navarro B, Lavigne M, Di Serio F, Kalantidis K, Katsarou K. PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation. FRONTIERS IN PLANT SCIENCE 2023; 14:1258023. [PMID: 38023875 PMCID: PMC10645062 DOI: 10.3389/fpls.2023.1258023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.
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Affiliation(s)
- Martha Tselika
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | | | - Paraskevi Kallemi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Matthieu Lavigne
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
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30
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Ohnishi Y, Kawashima T. Evidence of a novel silencing effect on transgenes in the Arabidopsis thaliana sperm cell. THE PLANT CELL 2023; 35:3926-3936. [PMID: 37602710 PMCID: PMC10615207 DOI: 10.1093/plcell/koad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
We encountered unexpected transgene silencing in Arabidopsis thaliana sperm cells; transgenes encoding proteins with no specific intracellular localization (cytoplasmic proteins) were silenced transcriptionally or posttranscriptionally. The mRNA of cytoplasmic protein transgenes tagged with a fluorescent protein gene was significantly reduced, resulting in undetectable fluorescent protein signals in the sperm cell. Silencing of the cytoplasmic protein transgenes in the sperm cell did not affect the expression of either its endogenous homologous genes or cotransformed transgenes encoding a protein with targeted intracellular localization. This transgene silencing in the sperm cell persisted in mutants of the major gene silencing machinery including DNA methylation. The incomprehensible, yet real, transgene silencing phenotypes occurring in the sperm cell could mislead the interpretation of experimental results in plant reproduction, and this Commentary calls attention to that risk and highlights details of this novel cytoplasmic protein transgene silencing.
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Affiliation(s)
- Yukinosuke Ohnishi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40503,USA
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40503,USA
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31
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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32
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Liu B, Zhao M. How transposable elements are recognized and epigenetically silenced in plants? CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102428. [PMID: 37481986 DOI: 10.1016/j.pbi.2023.102428] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
Abstract
Plant genomes are littered with transposable elements (TEs). Because TEs are potentially highly mutagenic, host organisms have evolved a set of defense mechanisms to recognize and epigenetically silence them. Although the maintenance of TE silencing is well studied, our understanding of the initiation of TE silencing is limited, but it clearly involves small RNAs and DNA methylation. Once TEs are silent, the silent state can be maintained to subsequent generations. However, under some circumstances, such inheritance is unstable, leading to the escape of TEs to the silencing machinery, resulting in the transcriptional activation of TEs. Epigenetic control of TEs has been found to be closely linked to many other epigenetic phenomena, such as genomic imprinting, and is known to contribute to regulation of genes, especially those near TEs. Here we review and discuss the current models of TE silencing, its unstable inheritance after hybridization, and the effects of epigenetic regulation of TEs on genomic imprinting.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
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33
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Zhang(张宇鹏) Y, Fan G, Toivainen T, Tengs T, Yakovlev I, Krokene P, Hytönen T, Fossdal CG, Grini PE. Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes. HORTICULTURE RESEARCH 2023; 10:uhad156. [PMID: 37719273 PMCID: PMC10500154 DOI: 10.1093/hr/uhad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Plants must adapt with increasing speed to global warming to maintain their fitness. One rapid adaptation mechanism is epigenetic memory, which may provide organisms sufficient time to adapt to climate change. We studied how the perennial Fragaria vesca adapted to warmer temperatures (28°C vs. 18°C) over three asexual generations. Differences in flowering time, stolon number, and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment. Induced methylome changes differed between the four ecotypes from Norway, Iceland, Italy, and Spain, but shared methylome responses were also identified. Most differentially methylated regions (DMRs) occurred in the CHG context, and most CHG and CHH DMRs were hypermethylated at the warmer temperature. In eight CHG DMR peaks, a highly similar methylation pattern could be observed between ecotypes. On average, 13% of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression. We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism, flowering time, and epigenetic mechanisms. Furthermore, we observed a negative correlation with gene expression when repetitive elements were found near (±2 kb) or inside genes. In conclusion, lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns. Both shared methylation patterns and transcriptome differences between F. vesca accessions were observed, indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.
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Affiliation(s)
- YuPeng Zhang(张宇鹏)
- EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Guangxun Fan
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Torstein Tengs
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Igor Yakovlev
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Paal Krokene
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland
| | - Carl Gunnar Fossdal
- Department of Molecular Plant Biology, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway
| | - Paul E. Grini
- EVOGENE, Department of Biosciences, University of Oslo, 0313 Oslo, Norway
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34
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Li Z, Liu Q, Zhao K, Cao D, Cao Z, Zhao K, Ma Q, Zhai G, Hu S, Li Z, Wang K, Gong F, Ma X, Zhang X, Ren R, Qiu D, Zhao Y, Yin D. Dynamic DNA methylation modification in peanut seed development. iScience 2023; 26:107062. [PMID: 37534185 PMCID: PMC10391728 DOI: 10.1016/j.isci.2023.107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 06/02/2023] [Indexed: 08/04/2023] Open
Abstract
Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1-35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development.
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Affiliation(s)
- Zhongfeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Kai Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Di Cao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Zenghui Cao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Kunkun Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Qian Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Gaidan Zhai
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Sasa Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Zhan Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Kuopeng Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Fangping Gong
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Xingli Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Xingguo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Rui Ren
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Ding Qiu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China
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Lehman TA, Rosas MA, Brew-Appiah RAT, Solanki S, York ZB, Dannay R, Wu Y, Roalson EH, Zheng P, Main D, Baskin TI, Sanguinet KA. BUZZ: an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon. THE NEW PHYTOLOGIST 2023. [PMID: 37421201 DOI: 10.1111/nph.19079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/10/2023] [Indexed: 07/10/2023]
Abstract
Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.
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Affiliation(s)
- Thiel A Lehman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Miguel A Rosas
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Zara B York
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Rachel Dannay
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Tobias I Baskin
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
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Vassilieff H, Geering ADW, Choisne N, Teycheney PY, Maumus F. Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes. Biomolecules 2023; 13:1069. [PMID: 37509105 PMCID: PMC10377300 DOI: 10.3390/biom13071069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
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Affiliation(s)
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre de La Réunion, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre de La Réunion, France
| | - Florian Maumus
- INRAE, URGI, Université Paris-Saclay, 78026 Versailles, France
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37
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Rowland L, Ramírez-Valiente JA, Hartley IP, Mencuccini M. How woody plants adjust above- and below-ground traits in response to sustained drought. THE NEW PHYTOLOGIST 2023. [PMID: 37306017 DOI: 10.1111/nph.19000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/01/2023] [Indexed: 06/13/2023]
Abstract
Future increases in drought severity and frequency are predicted to have substantial impacts on plant function and survival. However, there is considerable uncertainty concerning what drought adjustment is and whether plants can adjust to sustained drought. This review focuses on woody plants and synthesises the evidence for drought adjustment in a selection of key above-ground and below-ground plant traits. We assess whether evaluating the drought adjustment of single traits, or selections of traits that operate on the same plant functional axis (e.g. photosynthetic traits) is sufficient, or whether a multi-trait approach, integrating across multiple axes, is required. We conclude that studies on drought adjustments in woody plants might overestimate the capacity for adjustment to drier environments if spatial studies along gradients are used, without complementary experimental approaches. We provide evidence that drought adjustment is common in above-ground and below-ground traits; however, whether this is adaptive and sufficient to respond to future droughts remains uncertain for most species. To address this uncertainty, we must move towards studying trait integration within and across multiple axes of plant function (e.g. above-ground and below-ground) to gain a holistic view of drought adjustments at the whole-plant scale and how these influence plant survival.
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Affiliation(s)
- Lucy Rowland
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RJ, UK
| | | | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, EX4 4RJ, UK
| | - Maurizio Mencuccini
- CREAF, Campus de Bellaterra (UAB), Cerdanyola del Vallés, Barcelona, 08193, Spain
- ICREA, Barcelona, 08010, Spain
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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. FRONTIERS IN PLANT SCIENCE 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] [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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Vigneaud J, Kohler A, Sow MD, Delaunay A, Fauchery L, Guinet F, Daviaud C, Barry KW, Keymanesh K, Johnson J, Singan V, Grigoriev I, Fichot R, Conde D, Perales M, Tost J, Martin FM, Allona I, Strauss SH, Veneault-Fourrey C, Maury S. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. THE NEW PHYTOLOGIST 2023; 238:2561-2577. [PMID: 36807327 DOI: 10.1111/nph.18734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.
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Affiliation(s)
- Julien Vigneaud
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Annegret Kohler
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Mamadou Dia Sow
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Laure Fauchery
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Frederic Guinet
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Francis M Martin
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
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Panda K, Mohanasundaram B, Gutierrez J, McLain L, Castillo SE, Sheng H, Casto A, Gratacós G, Chakrabarti A, Fahlgren N, Pandey S, Gehan MA, Slotkin RK. The plant response to high CO 2 levels is heritable and orchestrated by DNA methylation. THE NEW PHYTOLOGIST 2023; 238:2427-2439. [PMID: 36918471 DOI: 10.1111/nph.18876] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/07/2023] [Indexed: 05/19/2023]
Abstract
Plant responses to abiotic environmental challenges are known to have lasting effects on the plant beyond the initial stress exposure. Some of these lasting effects are transgenerational, affecting the next generation. The plant response to elevated carbon dioxide (CO2 ) levels has been well studied. However, these investigations are typically limited to plants grown for a single generation in a high CO2 environment while transgenerational studies are rare. We aimed to determine transgenerational growth responses in plants after exposure to high CO2 by investigating the direct progeny when returned to baseline CO2 levels. We found that both the flowering plant Arabidopsis thaliana and seedless nonvascular plant Physcomitrium patens continue to display accelerated growth rates in the progeny of plants exposed to high CO2 . We used the model species Arabidopsis to dissect the molecular mechanism and found that DNA methylation pathways are necessary for heritability of this growth response. More specifically, the pathway of RNA-directed DNA methylation is required to initiate methylation and the proteins CMT2 and CMT3 are needed for the transgenerational propagation of this DNA methylation to the progeny plants. Together, these two DNA methylation pathways establish and then maintain a cellular memory to high CO2 exposure.
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Affiliation(s)
- Kaushik Panda
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Jorge Gutierrez
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Lauren McLain
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Hudanyun Sheng
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Anna Casto
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Gustavo Gratacós
- Department of Computer Science & Engineering, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Ayan Chakrabarti
- Department of Computer Science & Engineering, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Biological Sciences, University of Missouri, MO, 65211, Columbia, USA
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 343] [Impact Index Per Article: 343.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. THE PLANT CELL 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- 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, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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45
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Liu B, Yang D, Wang D, Liang C, Wang J, Lisch D, Zhao M. Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537008. [PMID: 37131670 PMCID: PMC10153178 DOI: 10.1101/2023.04.15.537008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene, Mop1 (mediator of paramutation1) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in both trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in the mop1 mutant, although the effects of this mutant varied depending on the location of the CHH DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in F1 plants did require Mop1, initiation of the changes in the epigenetic state of TCM DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is not dependent on RNA-directed DNA methylation.
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Affiliation(s)
- Beibei Liu
- Department of Biology, Miami University, Oxford, OH 45056
| | - Diya Yang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Dafang Wang
- Biology Department, Hofstra University, Hempstead, NY 11549
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
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46
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Zhang J, Xie Y, Zhang H, He C, Wang X, Cui Y, Heng Y, Lin Y, Gu R, Wang J, Fu J. Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height. Int J Mol Sci 2023; 24:ijms24119150. [PMID: 37298102 DOI: 10.3390/ijms24119150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/12/2023] Open
Abstract
Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.
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Affiliation(s)
- Jie Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Xiaoli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfang Heng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingchao Lin
- Key Laboratory of Molecular Genetics, Guizhou Institute of Tobacco Science, Guiyang 550081, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Otake K, Kugou K, Robertlee J, Ohzeki JI, Okazaki K, Hanano S, Takahashi S, Shibata D, Masumoto H. De novo induction of a DNA-histone H3K9 methylation loop on synthetic human repetitive DNA in cultured tobacco cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:668-682. [PMID: 36825961 DOI: 10.1111/tpj.16164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/19/2023] [Indexed: 05/10/2023]
Abstract
Genetic modifications in plants are crucial tools for fundamental and applied research. Transgene expression usually varies among independent lines or their progeny and is associated with the chromatin structure of the insertion site. Strategies based on understanding how to manipulate the epigenetic state of the inserted gene cassette would help to ensure transgene expression. Here, we report a strategy for chromatin manipulation by the artificial tethering of epigenetic effectors to a synthetic human centromeric repetitive DNA (alphoid DNA) platform in plant Bright-Yellow-2 (BY-2) culture cells. By tethering DNA-methyltransferase (Nicotiana tabacum DRM1), we effectively induced DNA methylation and histone methylation (H3K9me2) on the alphoid DNA platform. Tethering of the Arabidopsis SUVH9, which has been reported to lack histone methyltransferase activity, also induced a similar epigenetic state on the alphoid DNA in BY-2 cells, presumably by activating the RNA-dependent DNA methylation (RdDM) pathway. Our results emphasize that the interplay between DNA and histone methylation mechanisms is intrinsic to plant cells. We also found that once epigenetic modification states were induced by the tethering of either DRM1 or SUVH9, the modification was maintained even when the direct tethering of the effector was inhibited. Our system enables the analysis of more diverse epigenetic effectors and will help to elucidate the chromatin assembly mechanisms of plant cells.
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Affiliation(s)
- Koichiro Otake
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Kazuto Kugou
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Jekson Robertlee
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Jun-Ichirou Ohzeki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Koei Okazaki
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Shigeru Hanano
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Daisuke Shibata
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
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León-Ruiz J, Espinal-Centeno A, Blilou I, Scheres B, Arteaga-Vázquez M, Cruz-Ramírez A. RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development. PLANTA 2023; 257:105. [PMID: 37120771 DOI: 10.1007/s00425-023-04135-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
MAIN CONCLUSION Our study presents evidence for a novel mechanism for RBR function in transcriptional gene silencing by interacting with key players of the RdDM pathway in Arabidopsis and several plant clades. Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4-siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein-protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO-RBR background.
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Affiliation(s)
- Jesús León-Ruiz
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México
| | - Annie Espinal-Centeno
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México
| | - Ikram Blilou
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Ben Scheres
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mario Arteaga-Vázquez
- Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, 91090, Xalapa, México.
| | - Alfredo Cruz-Ramírez
- Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México.
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Wang T, Wang B, Hua X, Tang H, Zhang Z, Gao R, Qi Y, Zhang Q, Wang G, Yu Z, Huang Y, Zhang Z, Mei J, Wang Y, Zhang Y, Li Y, Meng X, Wang Y, Pan H, Chen S, Li Z, Shi H, Liu X, Deng Z, Chen B, Zhang M, Gu L, Wang J, Ming R, Yao W, Zhang J. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. NATURE PLANTS 2023; 9:554-571. [PMID: 36997685 DOI: 10.1038/s41477-023-01378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.
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Affiliation(s)
- Tianyou Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xiuting Hua
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiting Gao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, China
| | - Zehuai Yu
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yongji Huang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Mei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yihan Li
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xue Meng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjun Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haoran Pan
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihong Shi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinlong Liu
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
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Ortiz-Vasquez Q, León-Martínez G, Barragán-Rosillo C, González-Orozco E, Deans S, Aldridge B, Vickers M, Feng X, Vielle-Calzada JP. Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1123211. [PMID: 36993852 PMCID: PMC10040562 DOI: 10.3389/fpls.2023.1123211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/02/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Although DNA methylation patterns are generally considered to be faithfully inherited in Arabidopsis thaliana (Arabidopsis), there is evidence of reprogramming during both male and female gametogenesis. The gynoecium is the floral reproductive organ from which the ovules develop and generate meiotically derived cells that give rise to the female gametophyte. It is not known whether the gynoecium can condition genomic methylation in the ovule or the developing female gametophyte. METHODS We performed whole genome bisulfite sequencing to characterize the methylation patterns that prevail in the genomic DNA of pre-meiotic gynoecia of wild-type and three mutants defective in genes of the RNA-directed DNA methylation pathway (RdDM): ARGONAUTE4 (AGO4), ARGONAUTE9 (AGO9), and RNA-DEPENDENT RNA POLYMERASE6 (RDR6). RESULTS By globally analyzing transposable elements (TEs) and genes located across the Arabidopsis genome, we show that DNA methylation levels are similar to those of gametophytic cells rather than those of sporophytic organs such as seedlings and rosette leaves. We show that none of the mutations completely abolishes RdDM, suggesting strong redundancy within the methylation pathways. Among all, ago4 mutation has the strongest effect on RdDM, causing more CHH hypomethylation than ago9 and rdr6. We identify 22 genes whose DNA methylation is significantly reduced in ago4, ago9 and rdr6 mutants, revealing potential targets regulated by the RdDM pathway in premeiotic gyneocia. DISCUSSION Our results indicate that drastic changes in methylation levels in all three contexts occur in female reproductive organs at the sporophytic level, prior to the alternation of generations within the ovule primordium, offering a possibility to start identifying the function of specific genes acting in the establishment of the female gametophytic phase of the Arabidopsis life cycle.
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Affiliation(s)
- Quetzely Ortiz-Vasquez
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Gloria León-Martínez
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Carlos Barragán-Rosillo
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Eduardo González-Orozco
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Samuel Deans
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Billy Aldridge
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Guanajuato, Mexico
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