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López-Catalina A, Reverter A, Alexandre PA, Nguyen LT, González-Recio O. Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach. Epigenetics 2024; 19:2381856. [PMID: 39044410 PMCID: PMC11271077 DOI: 10.1080/15592294.2024.2381856] [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: 04/18/2024] [Accepted: 07/14/2024] [Indexed: 07/25/2024] Open
Abstract
Epigenetic marks do not follow the Mendelian laws of inheritance. The environment can alter the epigenotype of an individual when exposed to different external stressors. In lactating cows, the first stages of gestation overlap with the lactation peak, creating a negative energy balance that is difficult to overcome with diet. This negative energy balance could affect early embryo development that must compete with the mammary tissue for nutrients. We hypothesize that the methylation profiles of calves born to nonlactating heifers are different from those of calves born to lactating cows. We found 50,277 differentially methylated cytosines and 2,281 differentially methylated regions between these two groups of animals. A comethylation network was constructed to study the correlation between the phenotypes of the mothers and the epigenome of the calves, revealing 265 regions associated with the phenotypes. Our study revealed the presence of DMCs and DMRs in calves gestated by heifers and lactating cows, which were linked to the dam's lactation and the calves' ICAP and milk EBV. Gene-specific analysis highlighted associations with vasculature and organ morphogenesis and cell communication and signalling. These finding support the hypothesis that calves gestated by nonlactating mothers have a different methylation profile than those gestated by lactating cows.
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Affiliation(s)
- Adrián López-Catalina
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Crta. de la Coruña km 7.5, Madrid, Spain
- Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, Madrid, Spain
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Pamela A. Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), CSIC, Crta. de la Coruña km 7.5, Madrid, Spain
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2
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Marquez-Molins J, Cheng J, Corell-Sierra J, Juarez-Gonzalez VT, Villalba-Bermell P, Annacondia ML, Gomez G, Martinez G. Hop stunt viroid infection induces heterochromatin reorganization. THE NEW PHYTOLOGIST 2024; 243:2351-2367. [PMID: 39030826 DOI: 10.1111/nph.19986] [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: 03/02/2024] [Accepted: 06/26/2024] [Indexed: 07/22/2024]
Abstract
Viroids are pathogenic noncoding RNAs that completely rely on their host molecular machinery to accomplish their life cycle. Several interactions between viroids and their host molecular machinery have been identified, including interference with epigenetic mechanisms such as DNA methylation. Despite this, whether viroids influence changes in other epigenetic marks such as histone modifications remained unknown. Epigenetic regulation is particularly important during pathogenesis processes because it might be a key regulator of the dynamism of the defense response. Here we have analyzed the changes taking place in Cucumis sativus (cucumber) facultative and constitutive heterochromatin during hop stunt viroid (HSVd) infection using chromatin immunoprecipitation (ChIP) of the two main heterochromatic marks: H3K9me2 and H3K27me3. We find that HSVd infection is associated with changes in both H3K27me3 and H3K9me2, with a tendency to decrease the levels of repressive epigenetic marks through infection progression. These epigenetic changes are connected to the transcriptional regulation of their expected targets, genes, and transposable elements. Indeed, several genes related to the defense response are targets of both epigenetic marks. Our results highlight another host regulatory mechanism affected by viroid infection, providing further information about the complexity of the multiple layers of interactions between pathogens/viroids and hosts/plants.
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Affiliation(s)
- Joan Marquez-Molins
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Jinping Cheng
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Julia Corell-Sierra
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
| | - Pascual Villalba-Bermell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - Maria Luz Annacondia
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, 1871, Denmark
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), University of Valencia (UV), Paterna, 46980, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, 75007, Sweden
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3
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Zeng Y, Somers J, Bell HS, Vejlupkova Z, Dawe RK, Fowler JE, Nelms B, Gent JI. Potent pollen gene regulation by DNA glycosylases in maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580204. [PMID: 38405940 PMCID: PMC10888782 DOI: 10.1101/2024.02.13.580204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Although DNA methylation primarily represses TEs, it also represses select genes that are methylated in plant body tissues but demethylated by DNA glycosylases (DNGs) in endosperm or pollen. Activity of either one of two DNGs, MDR1 or DNG102, is essential for pollen viability in maize. Using single-pollen mRNA sequencing on pollen segregating mutations in both genes, we identified 58 candidate DNG target genes that account for 11.1% of the wild-type transcriptome but are silent or barely detectable in the plant body (sporophyte). They are unusual in their tendency to lack introns but even more so in their having TE-like methylation in their CDS. The majority have predicted functions in cell wall modification, and they likely support the rapid tip growth characteristic of pollen tubes. These results suggest a critical role for DNA methylation and demethylation in regulating maize genes with potential for extremely high expression in pollen but constitutive silencing elsewhere.
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Bubb KL, Hamm MO, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Vollger MR, Trapnell C, Cuperus JT, Queitsch C, Stergachis AB. The regulatory potential of transposable elements in maize. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602892. [PMID: 39026747 PMCID: PMC11257541 DOI: 10.1101/2024.07.10.602892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Since their initial discovery in maize, transposable elements (TEs) have emerged as being integral to the evolution of maize, accounting for 80% of its genome. However, the repetitive nature of TEs has hindered our understanding of their regulatory potential. Here, we demonstrate that long-read chromatin fiber sequencing (Fiber-seq) permits the comprehensive annotation of the regulatory potential of maize TEs. We uncover that only 94 LTR retrotransposons contain the functional epigenetic architecture required for mobilization within maize leaves. This epigenetic architecture degenerates with evolutionary age, resulting in solo TE enhancers being preferentially marked by simultaneous hyper-CpG methylation and chromatin accessibility, an architecture markedly divergent from canonical enhancers. We find that TEs shape maize gene regulation by creating novel promoters within the TE itself as well as through TE-mediated gene amplification. Lastly, we uncover a pervasive epigenetic code directing TEs to specific loci, including that locus that sparked McClintock's discovery of TEs.
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Affiliation(s)
- Kerry L. Bubb
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Morgan O. Hamm
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joseph K. Min
- Department of Genome Sciences, University of Washington, Seattle, USA
| | | | - Nicholas A. Mueth
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Jane Ranchalis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R. Vollger
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, USA
- Molecular & Cellular Biology Program, University of Washington, Seattle, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA
| | - Josh T. Cuperus
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, USA
- Molecular & Cellular Biology Program, University of Washington, Seattle, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA
| | - Andrew B. Stergachis
- Department of Genome Sciences, University of Washington, Seattle, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
- Molecular & Cellular Biology Program, University of Washington, Seattle, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, USA
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5
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Afreen U, Kumar M. 5-mC methylation study of sORFs in 3'UTR of transcription factor JUNGBRUNNEN 1-like during leaf rust pathogenesis in wheat. Mol Biol Rep 2024; 51:801. [PMID: 39001882 DOI: 10.1007/s11033-024-09718-9] [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: 03/13/2024] [Accepted: 06/11/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND JUB1, a NAC domain containing hydrogen peroxide-induced transcription factor, plays a critical role in plant immunity. Little is known about how JUB1 responds to leaf rust disease in wheat. Recent discoveries in genomics have also unveiled a multitude of sORFs often assumed to be non-functional, to argue for the necessity of including them as potential regulatory players of translation. However, whether methylation on sORFs spanning the 3'UTR of regulatory genes like JUB1 modulate gene expression, remains unclear. METHODS AND RESULTS In this study, we identified the methylation states of two sORFs in 3'UTR of a homologous gene of JUB1 in wheat, TaJUB1-L, at cytosine residues in CpG, CHH and CHG sites at different time points of disease progression in two near-isogenic lines of wheat (HD2329), with and without Lr24 gene during leaf rust pathogenesis. Here, we report a significant demethylation of the CpG dinucleotides occurring in the sORFs of the 3'UTR in the resistant isolines after 24 h post-infection. Also, the up-regulated gene expression observed through RT-qPCR was directly proportional to the demethylation of the CpG sites in the sORFs. CONCLUSIONS Our findings indicate that TaJUB1-L might be a positive regulator in providing tolerance during leaf rust pathogenesis and cytosine methylation at 3'UTR might act as a switch for its expression control. These results enrich the potential benefit of conventional methylation assay techniques for unraveling the unexplored enigma in epigenetics during plant-pathogen interaction in a cost-effective and confidentially conclusive manner.
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Affiliation(s)
- Uzma Afreen
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Guerrero L, Bay R. Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral. Evol Appl 2024; 17:e13757. [PMID: 39027686 PMCID: PMC11254580 DOI: 10.1111/eva.13757] [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] [Received: 08/02/2023] [Revised: 06/21/2024] [Accepted: 06/29/2024] [Indexed: 07/20/2024] Open
Abstract
Phenotypic plasticity can buffer organisms against short-term environmental fluctuations. For example, previous exposure to increased temperatures can increase thermal tolerance in many species. Prior studies have found that acclimation to higher temperature can influence the magnitude of transcriptional response to subsequent acute thermal stress (hereafter, "transcriptional response modulation"). However, mechanisms mediating this gene expression response and, ultimately, phenotypic plasticity remain largely unknown. Epigenetic modifications are good candidates for modulating transcriptional response, as they broadly correlate with gene expression. Here, we investigate changes in DNA methylation as a possible mechanism controlling shifts in gene expression plasticity and thermal acclimation in the reef-building coral Acropora nana. We find that gene expression response to acute stress is altered in corals acclimated to different temperatures, with many genes exhibiting a dampened response to heat stress in corals pre-conditioned to higher temperatures. At the same time, we observe shifts in methylation during both acclimation (11 days) and acute heat stress (24 h). We observed that the acute heat stress results in shifts in gene-level methylation and elicits an acute transcriptional response in distinct gene sets. Further, acclimation-induced shifts in gene expression plasticity and differential methylation also largely occur in separate sets of genes. Counter to our initial hypothesis no overall correlation between the magnitude of differential methylation and the change in gene expression plasticity. We do find a small but statistically significant overlap in genes exhibiting both dampened expression response and shifts in methylation (14 genes), which could be candidates for further inquiry. Overall, our results suggest transcriptional response modulation occurs independently from methylation changes induced by thermal acclimation.
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Affiliation(s)
| | - Rachael Bay
- University of California, DavisDavisCaliforniaUSA
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Baduel P, Sammarco I, Barrett R, Coronado‐Zamora M, Crespel A, Díez‐Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome and the environment. Evol Appl 2024; 17:e13730. [PMID: 39050763 PMCID: PMC11266121 DOI: 10.1111/eva.13730] [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: 11/01/2023] [Revised: 03/30/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024] Open
Abstract
The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale SupérieurePSL University, CNRSParisFrance
| | - Iris Sammarco
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Rowan Barrett
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | | | | | | | - Janay Fox
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Dario Galanti
- Institute of Evolution and Ecology (EvE)University of TuebingenTübingenGermany
| | | | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Eric Wootton
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Ewan Harney
- Institute of Evolutionary BiologyCSIC, UPFBarcelonaSpain
- School of BiosciencesUniversity of SheffieldSheffieldUK
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8
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Briffa A, Menon G, Movilla Miangolarra A, Howard M. Dissecting Mechanisms of Epigenetic Memory Through Computational Modeling. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:265-290. [PMID: 38424070 DOI: 10.1146/annurev-arplant-070523-041445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Understanding the mechanistic basis of epigenetic memory has proven to be a difficult task due to the underlying complexity of the systems involved in its establishment and maintenance. Here, we review the role of computational modeling in helping to unlock this complexity, allowing the dissection of intricate feedback dynamics. We focus on three forms of epigenetic memory encoded in gene regulatory networks, DNA methylation, and histone modifications and discuss the important advantages offered by plant systems in their dissection. We summarize the main modeling approaches involved and highlight the principal conceptual advances that the modeling has enabled through iterative cycles of predictive modeling and experiments. Lastly, we discuss remaining gaps in our understanding and how intertwined theory and experimental approaches might help in their resolution.
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Affiliation(s)
- Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom;
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom;
| | - Ander Movilla Miangolarra
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom;
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom;
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9
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Yu G, Zhang B, Chen Q, Huang Z, Zhang B, Wang K, Han J. Dynamic DNA methylation modifications in the cold stress response of cassava. Genomics 2024; 116:110871. [PMID: 38806102 DOI: 10.1016/j.ygeno.2024.110871] [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: 03/09/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/30/2024]
Abstract
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Baowang Zhang
- Qingdao Smart Rural Development Service Center, Qingdao 266000, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Zequan Huang
- Xinglin College, Nantong University, Qidong 226236, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China.
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10
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Zhang Y, Jang H, Luo Z, Dong Y, Xu Y, Kantamneni Y, Schmitz RJ. Dynamic evolution of the heterochromatin sensing histone demethylase IBM1. PLoS Genet 2024; 20:e1011358. [PMID: 38991029 PMCID: PMC11265718 DOI: 10.1371/journal.pgen.1011358] [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: 03/04/2024] [Revised: 07/23/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Heterochromatin is critical for maintaining genome stability, especially in flowering plants, where it relies on a feedback loop involving the H3K9 methyltransferase, KRYPTONITE (KYP), and the DNA methyltransferase CHROMOMETHYLASE3 (CMT3). The H3K9 demethylase INCREASED IN BONSAI METHYLATION 1 (IBM1) counteracts the detrimental consequences of KYP-CMT3 activity in transcribed genes. IBM1 expression in Arabidopsis is uniquely regulated by methylation of the 7th intron, allowing it to monitor global H3K9me2 levels. We show the methylated intron is prevalent across flowering plants and its underlying sequence exhibits dynamic evolution. We also find extensive genetic and expression variations in KYP, CMT3, and IBM1 across flowering plants. We identify Arabidopsis accessions resembling weak ibm1 mutants and Brassicaceae species with reduced IBM1 expression or deletions. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity and loss of gene body DNA methylation, as cmt3 mutants in A. thaliana mitigate the deleterious effects of IBM1.
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Affiliation(s)
- Yinwen Zhang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Ziliang Luo
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yinxin Dong
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yangyang Xu
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yamini Kantamneni
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
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11
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Carballo J, Achilli A, Hernández F, Bocchini M, Pasten MC, Marconi G, Albertini E, Zappacosta D, Echenique V. Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes. PLANT REPRODUCTION 2024; 37:133-145. [PMID: 38055074 PMCID: PMC11180019 DOI: 10.1007/s00497-023-00490-7] [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: 07/01/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. Eragrostis curvula is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in E. curvula genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.
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Affiliation(s)
- J Carballo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - A Achilli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - F Hernández
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
| | - M Bocchini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy
| | - M C Pasten
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
| | - G Marconi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy
| | - E Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, 06121, Perugia, Italy.
| | - D Zappacosta
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina.
| | - V Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CCT-CONICET Bahía Blanca), Camino de La Carrindanga Km 7, 8000, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina.
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Boissinot J, Adamek K, Jones AMP, Normandeau E, Boyle B, Torkamaneh D. Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population. FRONTIERS IN PLANT SCIENCE 2024; 15:1381154. [PMID: 38872884 PMCID: PMC11169872 DOI: 10.3389/fpls.2024.1381154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.
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Affiliation(s)
- Justin Boissinot
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut intelligence et données (IID), Université Laval, Québec, QC, Canada
| | - Kristian Adamek
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Davoud Torkamaneh
- Département de phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec, QC, Canada
- Institut intelligence et données (IID), Université Laval, Québec, QC, Canada
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13
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Shi T, Zhang X, Hou Y, Jia C, Dan X, Zhang Y, Jiang Y, Lai Q, Feng J, Feng J, Ma T, Wu J, Liu S, Zhang L, Long Z, Chen L, Street NR, Ingvarsson PK, Liu J, Yin T, Wang J. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. MOLECULAR PLANT 2024; 17:725-746. [PMID: 38486452 DOI: 10.1016/j.molp.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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Affiliation(s)
- Tingting Shi
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xinxin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yukang Hou
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changfu Jia
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuming Dan
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Lai
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiajun Feng
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jianju Feng
- College of Horticulture and Forestry, Tarim University, Alar 843300, China
| | - Tao Ma
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jiali Wu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Shuyu Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Lei Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zhiqin Long
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Liyang Chen
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Västerbotten, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, Jiangsu, China.
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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14
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Sacchi B, Humphries Z, Kružlicová J, Bodláková M, Pyne C, Choudhury BI, Gong Y, Bačovský V, Hobza R, Barrett SCH, Wright SI. Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus. Mol Biol Evol 2024; 41:msae074. [PMID: 38606901 PMCID: PMC11057207 DOI: 10.1093/molbev/msae074] [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: 10/06/2023] [Revised: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.
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Affiliation(s)
- Bianca Sacchi
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Zoë Humphries
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Markéta Bodláková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Cassandre Pyne
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Baharul I Choudhury
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Biology, Queen’s University, Kingston, Canada
| | - Yunchen Gong
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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15
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He X, Chen Y, Xia Y, Hong X, You H, Zhang R, Liang Z, Cui Q, Zhang S, Zhou M, Yang D. DNA methylation regulates biosynthesis of tanshinones and phenolic acids during growth of Salvia miltiorrhiza. PLANT PHYSIOLOGY 2024; 194:2086-2100. [PMID: 37879117 DOI: 10.1093/plphys/kiad573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
DNA methylation plays a crucial role in the regulation of plant growth and the biosynthesis of secondary metabolites. Danshen (Salvia miltiorrhiza) is a valuable Chinese herbal medicine commonly used to treat cardiovascular diseases; its active ingredients are tanshinones and phenolic acids, which primarily accumulate in roots. Here, we conducted a targeted metabolic analysis of S. miltiorrhiza roots at 3 distinct growth stages: 40 d old (r40), 60 d old (r60), and 90 d old (r90). The contents of tanshinones (cryptotanshinone, tanshinone I, tanshinone IIA, and rosmariquinone) and phenolic acids (rosmarinic acid and salvianolic acid B) gradually increased during plant development. Whole-genome bisulfite sequencing and transcriptome sequencing of roots at the 3 growth stages revealed an increased level of DNA methylation in the CHH context (H represents A, T, or C) context at r90 compared with r40 and r60. Increased DNA methylation levels were associated with elevated expression of various genes linked to epigenetic regulations, including CHROMOMETHYLASE2 (SmCMT2), Decrease in DNA Methylation 1 (SmDDM1), Argonaute 4 (SmAGO4), and DOMAINS REARRANGED METHYLTRANSFERASE 1 (SmDRM1). Moreover, expression levels of many genes involved in tanshinone and salvianolic acid biosynthesis, such as copalyldiphosphate synthase 5 (SmCPS5), cytochrome P450-related enzyme (SmCYP71D464), geranylgeranyl diphosphate synthase (SmGGPPS1), geranyl diphosphate synthase (SmGPPS), hydroxyphenylpyruvate reductase (SmHPPR), and hydroxyphenylpyruvate dioxygenase (SmHPPD), were altered owing to hyper-methylation, indicating that DNA methylation plays an important role in regulating tanshinone and phenolic acid accumulation. Our data shed light on the epigenetic regulation of root growth and the biosynthesis of active ingredients in S. miltiorrhiza, providing crucial clues for further improvement of active compound production via molecular breeding in S. miltiorrhiza.
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Affiliation(s)
- Xinyu He
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yiwen Chen
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yuting Xia
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xinyu Hong
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Huaqian You
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Rui Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zongsuo Liang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Qi Cui
- Laboratory of Ornamental Plants, Department of Landscape Architecture, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Shuncang Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dongfeng Yang
- College of Life Sciences and Medicine, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, China
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16
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Yuditskiy K, Bezdvornykh I, Kazantseva A, Kanapin A, Samsonova A. BSXplorer: analytical framework for exploratory analysis of BS-seq data. BMC Bioinformatics 2024; 25:96. [PMID: 38438881 PMCID: PMC10913661 DOI: 10.1186/s12859-024-05722-9] [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: 11/16/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily. RESULTS BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication. CONCLUSIONS BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.
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Affiliation(s)
- Konstantin Yuditskiy
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia, 199004
| | - Igor Bezdvornykh
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia, 199004
| | - Anastasiya Kazantseva
- Laboratory of Neurocognitive Genomics, Department of Genetics and Fundamental Medicine, Ufa University of Science and Technology, Ufa, Russia, 450076
| | - Alexander Kanapin
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia, 199004
| | - Anastasia Samsonova
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia, 199004.
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17
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Han M, Lin S, Zhu B, Tong W, Xia E, Wang Y, Yang T, Zhang S, Wan X, Liu J, Niu Q, Zhu J, Bao S, Zhang Z. Dynamic DNA Methylation Regulates Season-Dependent Secondary Metabolism in the New Shoots of Tea Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3984-3997. [PMID: 38357888 DOI: 10.1021/acs.jafc.3c08568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Plant secondary metabolites are critical quality-conferring compositions of plant-derived beverages, medicines, and industrial materials. The accumulations of secondary metabolites are highly variable among seasons; however, the underlying regulatory mechanism remains unclear, especially in epigenetic regulation. Here, we used tea plants to explore an important epigenetic mark DNA methylation (5mC)-mediated regulation of plant secondary metabolism in different seasons. Multiple omics analyses were performed on spring and summer new shoots. The results showed that flavonoids and theanine metabolism dominated in the metabolic response to seasons in the new shoots. In summer new shoots, the genes encoding DNA methyltransferases and demethylases were up-regulated, and the global CG and CHG methylation reduced and CHH methylation increased. 5mC methylation in promoter and gene body regions influenced the seasonal response of gene expression; the amplitude of 5mC methylation was highly correlated with that of gene transcriptions. These differentially methylated genes included those encoding enzymes and transcription factors which play important roles in flavonoid and theanine metabolic pathways. The regulatory role of 5mC methylation was further verified by applying a DNA methylation inhibitor. These findings highlight that dynamic DNA methylation plays an important role in seasonal-dependent secondary metabolism and provide new insights for improving tea quality.
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Affiliation(s)
- Mengxue Han
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shijia Lin
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Biying Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Yuanrong Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Tianyuan Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Shupei Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
| | - Jianjun Liu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
- Key Laboratory of Tea Biology and Tea Processing of Ministry of Agriculture and Rural Affairs, Hefei, Anhui 230036, China
- International Joint Research Laboratory of Tea Chemistry and Health Effects of Ministry of Education, Hefei, Anhui 230036, China
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18
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Runemark A, Moore EC, Larson EL. Hybridization and gene expression: Beyond differentially expressed genes. Mol Ecol 2024:e17303. [PMID: 38411307 DOI: 10.1111/mec.17303] [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: 12/03/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
| | - Emily C Moore
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, Colorado, USA
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19
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Yadav S, Meena S, Kalwan G, Jain PK. DNA methylation: an emerging paradigm of gene regulation under drought stress in plants. Mol Biol Rep 2024; 51:311. [PMID: 38372841 DOI: 10.1007/s11033-024-09243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024]
Abstract
Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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20
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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] [Grants] [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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Dainelli M, Castellani MB, Pignattelli S, Falsini S, Ristori S, Papini A, Colzi I, Coppi A, Gonnelli C. Growth, physiological parameters and DNA methylation in Spirodela polyrhiza (L.) Schleid exposed to PET micro-nanoplastic contaminated waters. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108403. [PMID: 38290343 DOI: 10.1016/j.plaphy.2024.108403] [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: 09/22/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
The effects of polyethylene terephthalate micro-nanoplastics (PET-MNPs) were tested on the model freshwater species Spirodela polyrhiza (L.) Schleid., with focus on possible particle-induced epigenetic effects (i.e. alteration of DNA methylation status). MNPs (size ∼ 200-300 nm) were produced as water dispersions from PET bottles through repeated cycles of homogenization and used to prepare N-medium at two environmentally relevant concentrations (∼0.05 g L-1 and ∼0.1 g L-1 of MNPs). After 10 days of exposure, a reduction in fresh and dry weight was observed in treated plants, even if the average specific growth rate for both frond number and area was not altered. Impaired growth was coupled with a MNP-induced decrease of chlorophyll fluorescence parameters (i.e. ΨETo and Piabs, indicators of photochemical efficiency) and starch concentration, as well as with alterations in plant ionomic profile and oxidative status. The methylation-sensitive amplification polymorphism (MSAP) technique was used to assess possible changes in DNA methylation levels induced by plastic particles. The analysis showed unusual hypermethylation in 5'-CCGG sites that could be implicated in DNA protection from dangerous agents (i.e. reactive oxygen species) or in the formation of new epialleles. This work represents the first evidence of MNP-induced epigenetic modifications in the plant world.
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Affiliation(s)
- Marco Dainelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Maria Beatrice Castellani
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Pignattelli
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Sara Falsini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Sandra Ristori
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Firenze, Italy
| | - Alessio Papini
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Ilaria Colzi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy.
| | - Andrea Coppi
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
| | - Cristina Gonnelli
- Department of Biology, Università degli Studi di Firenze, via Micheli 1, 50121, Florence, Italy
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22
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Orłowska R, Zimny J, Zebrowski J, Androsiuk P, Bednarek PT. An insight into tissue culture-induced variation origin shared between anther culture-derived triticale regenerants. BMC PLANT BIOLOGY 2024; 24:43. [PMID: 38200422 PMCID: PMC10782687 DOI: 10.1186/s12870-023-04679-w] [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: 06/19/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND The development of the plant in vitro techniques has brought about the variation identified in regenerants known as somaclonal or tissue culture-induced variation (TCIV). S-adenosyl-L-methionine (SAM), glutathione (GSH), low methylated pectins (LMP), and Cu(II) ions may be implicated in green plant regeneration efficiency (GPRE) and TCIV, according to studies in barley (Hordeum vulgare L.) and partially in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927). Using structural equation models (SEM), these metabolites have been connected to the metabolic pathways (Krebs and Yang cycles, glycolysis, transsulfuration), but not for triticale. Using metabolomic and (epi)genetic data, the study sought to develop a triticale regeneration efficiency statistical model. The culture's induction medium was supplemented with various quantities of Cu(II) and Ag(I) ions for regeneration. The period of plant regeneration has also changed. The donor plant, anther-derived regenerants, and metAFLP were utilized to analyze TCIV concerning DNA in symmetric (CG, CHG) and asymmetric (CHH) sequence contexts. Attenuated Total Reflectance-Fourier Transfer Infrared (ATR-FTIR) spectroscopy was used to gather the metabolomic information on LMP, SAM, and GSH. To frame the data, a structural equation model was employed. RESULTS According to metAFLP analysis, the average sequence change in the CHH context was 8.65%, and 0.58% was de novo methylation. Absorbances of FTIR spectra in regions specific for LMP, SAM, and GSH were used as variables values introduced to the SEM model. The average number of green regenerants per 100 plated anthers was 2.55. CONCLUSIONS The amounts of pectin demethylation, SAM, de novo methylation, and GSH are connected in the model to explain GPRE. By altering the concentration of Cu(II) ions in the medium, which influences the amount of pectin, triticale's GPRE can be increased.
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Affiliation(s)
- Renata Orłowska
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Janusz Zimny
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland
| | - Jacek Zebrowski
- Institute of Biotechnology, College of Natural Science, University of Rzeszow, Al. Rejtana 16c, Rzeszow, 35-959, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-719, Poland
| | - Piotr T Bednarek
- Plant Breeding and Acclimatization Institute, National Research Institute, Radzików, Błonie, 05-870, Poland.
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23
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Kho J, Delgado ML, McCracken GR, Munden J, Ruzzante DE. Epigenetic patterns in Atlantic herring (Clupea harengus): Temperature and photoperiod as environmental stressors during larval development. Mol Ecol 2024; 33:e17187. [PMID: 37909655 DOI: 10.1111/mec.17187] [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: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Understanding the molecular mechanisms underlying individual responses to environmental changes is crucial for species conservation and management. Pelagic fishes including Atlantic herring (Clupea harengus) are of particular interest because of their key ecological and economic roles and their susceptibility to a changing ocean from global warming. Temperature and photoperiod have been linked with spawning time and location in adult herring, but no study has thus far investigated the role of environmental factors on gene regulation during the vulnerable early developmental stages. Here, we examine DNA methylation patterns of larval herring bred under two temperatures (11°C and 13°C) and photoperiod (6 and 12 h) regimes in a 2 × 2 factorial design. We found consistently high levels of global methylation across all individuals and a decline in global methylation with increased developmental stage that was more pronounced at 13°C (p ≤ 0.007) than at 11°C (p ≥ 0.21). Most of the differentially methylated sites were in exon and promoter regions for genes linked to metabolism and development, some of which were hypermethylated at higher temperature. These results demonstrate the important role of DNA methylation during larval development and suggest that this molecular mechanism might be key in regulating early-stage responses to environmental stressors in Atlantic herring.
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Affiliation(s)
- J Kho
- Department of Biology, Dalhousie University, Halifax, Canada
| | - M L Delgado
- Department of Biology, Dalhousie University, Halifax, Canada
| | - G R McCracken
- Department of Biology, Dalhousie University, Halifax, Canada
| | - J Munden
- Herring Science Council, Halifax, Canada
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Canada
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24
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de Carvalho CF, Slate J, Villoutreix R, Soria-Carrasco V, Riesch R, Feder JL, Gompert Z, Nosil P. DNA methylation differences between stick insect ecotypes. Mol Ecol 2023; 32:6809-6823. [PMID: 37864542 DOI: 10.1111/mec.17165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e. ecotypes). By integrating results from sequencing of whole transcriptomes, genomes and methylomes, we investigate whether environmental, host and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in the CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, with methylation being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies.
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Affiliation(s)
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
| | | | | | - Rüdiger Riesch
- University of Montpellier, CEFE, CNRS, EPHE, IRD, Montpellier, France
- Department of Biological Sciences, Centre for Ecology, Evolution and Behaviour, Royal Holloway University of London, Egham, UK
| | - Jeffrey L Feder
- Department of Biology, Notre Dame University, South Bend, Indiana, USA
| | | | - Patrik Nosil
- School of Biosciences, University of Sheffield, Sheffield, UK
- University of Montpellier, CEFE, CNRS, EPHE, IRD, Montpellier, France
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25
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Martin GT, Solares E, Guadardo-Mendez J, Muyle A, Bousios A, Gaut BS. miRNA-like secondary structures in maize ( Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression. Genome Res 2023; 33:1932-1946. [PMID: 37918960 PMCID: PMC10760457 DOI: 10.1101/gr.277459.122] [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: 11/07/2022] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
RNA molecules carry information in their primary sequence and also their secondary structure. Secondary structure can confer important functional information, but it is also a signal for an RNAi-like host epigenetic response mediated by small RNAs (smRNAs). In this study, we used two bioinformatic methods to predict local secondary structures across features of the maize genome, focusing on small regions that had similar folding properties to pre-miRNA loci. We found miRNA-like secondary structures to be common in genes and most, but not all, superfamilies of RNA and DNA transposable elements (TEs). The miRNA-like regions map to a higher diversity of smRNAs than regions without miRNA-like structure, explaining up to 27% of variation in smRNA mapping for some TE superfamilies. This mapping bias is more pronounced among putatively autonomous TEs relative to nonautonomous TEs. Genome-wide, miRNA-like regions are also associated with elevated methylation levels, particularly in the CHH context. Among genes, those with miRNA-like secondary structure are 1.5-fold more highly expressed, on average, than other genes. However, these genes are also more variably expressed across the 26 nested association mapping founder lines, and this variability positively correlates with the number of mapping smRNAs. We conclude that local miRNA-like structures are a nearly ubiquitous feature of expressed regions of the maize genome, that they correlate with higher smRNA mapping and methylation, and that they may represent a trade-off between functional requirements and the potentially negative consequences of smRNA production.
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Affiliation(s)
- Galen T Martin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92617, USA
| | - Edwin Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92617, USA
- Department of Ecology and Evolutionary Biology, University of California, Davis, California 95616, USA
| | - Jeanelle Guadardo-Mendez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92617, USA
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92617, USA
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 34090 Montpellier, France
| | - Alexandros Bousios
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92617, USA;
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26
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Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Syst 2023; 14:953-967.e17. [PMID: 37944515 DOI: 10.1016/j.cels.2023.10.007] [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: 10/03/2022] [Revised: 07/18/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
Abstract
Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.
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Affiliation(s)
- Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Elizabeth Hollwey
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria
| | - Zaigham Shahzad
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Jonathan D Moore
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - David B Lyons
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Daniel Zilberman
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK; Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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27
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Zeng Y, Dawe RK, Gent JI. Natural methylation epialleles correlate with gene expression in maize. Genetics 2023; 225:iyad146. [PMID: 37556604 PMCID: PMC10550312 DOI: 10.1093/genetics/iyad146] [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: 02/22/2023] [Revised: 02/22/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
DNA methylation in plants is depleted from cis-regulatory elements in and near genes but is present in some gene bodies, including exons. Methylation in exons solely in the CG context is called gene body methylation (gbM). Methylation in exons in both CG and non-CG contexts is called TE-like methylation (teM). Assigning functions to both forms of methylation in genes has proven to be challenging. Toward that end, we utilized recent genome assemblies, gene annotations, transcription data, and methylome data to quantify common patterns of gene methylation and their relations to gene expression in maize. We found that gbM genes exist in a continuum of CG methylation levels without a clear demarcation between unmethylated genes and gbM genes. Analysis of expression levels across diverse maize stocks and tissues revealed a weak but highly significant positive correlation between gbM and gene expression except in endosperm. gbM epialleles were associated with an approximately 3% increase in steady-state expression level relative to unmethylated epialleles. In contrast to gbM genes, which were conserved and were broadly expressed across tissues, we found that teM genes, which make up about 12% of genes, are mainly silent, are poorly conserved, and exhibit evidence of annotation errors. We used these data to flag teM genes in the 26 NAM founder genome assemblies. While some teM genes are likely functional, these data suggest that the majority are not, and their inclusion can confound the interpretation of whole-genome studies.
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Affiliation(s)
- Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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Troyee AN, Peña-Ponton C, Medrano M, Verhoeven KJF, Alonso C. Herbivory induced methylation changes in the Lombardy poplar: A comparison of results obtained by epiGBS and WGBS. PLoS One 2023; 18:e0291202. [PMID: 37682835 PMCID: PMC10490839 DOI: 10.1371/journal.pone.0291202] [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: 03/31/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
DNA cytosine methylation is an epigenetic mechanism involved in regulation of plant responses to biotic and abiotic stress and its ability to change can vary with the sequence context in which a cytosine appears (CpG, CHG, CHH, where H = Adenine, Thymine, Cytosine). Quantification of DNA methylation in model plant species is frequently addressed by Whole Genome Bisulfite Sequencing (WGBS), which requires a good-quality reference genome. Reduced Representation Bisulfite Sequencing (RRBS) is a cost-effective potential alternative for ecological research with limited genomic resources and large experimental designs. In this study, we provide for the first time a comprehensive comparison between the outputs of RRBS and WGBS to characterize DNA methylation changes in response to a given environmental factor. In particular, we used epiGBS (recently optimized RRBS) and WGBS to assess global and sequence-specific differential methylation after insect and artificial herbivory in clones of Populus nigra cv. 'italica'. We found that, after any of the two herbivory treatments, global methylation percentage increased in CHH, and the shift was detected as statistically significant only by epiGBS. As regards to loci-specific differential methylation induced by herbivory (cytosines in epiGBS and regions in WGBS), both techniques indicated the specificity of the response elicited by insect and artificial herbivory, together with higher frequency of hypo-methylation in CpG and hyper-methylation in CHH. Methylation changes were mainly found in gene bodies and intergenic regions when present at CpG and CHG and in transposable elements and intergenic regions at CHH context. Thus, epiGBS succeeded to characterize global, genome-wide methylation changes in response to herbivory in the Lombardy poplar. Our results support that epiGBS could be particularly useful in large experimental designs aimed to explore epigenetic changes of non-model plant species in response to multiple environmental factors.
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Affiliation(s)
- A. Niloya Troyee
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
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29
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Alejo-Jacuinde G, Nájera-González HR, Chávez Montes RA, Gutierrez Reyes CD, Barragán-Rosillo AC, Perez Sanchez B, Mechref Y, López-Arredondo D, Yong-Villalobos L, Herrera-Estrella L. Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism. Commun Biol 2023; 6:820. [PMID: 37550387 PMCID: PMC10406817 DOI: 10.1038/s42003-023-05192-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
Chia (Salvia hispanica) is an emerging crop considered a functional food containing important substances with multiple potential applications. However, the molecular basis of some relevant chia traits, such as seed mucilage and polyphenol content, remains to be discovered. This study generates an improved chromosome-level reference of the chia genome, resolving some highly repetitive regions, describing methylation patterns, and refining genome annotation. Transcriptomic analysis shows that seeds exhibit a unique expression pattern compared to other organs and tissues. Thus, a metabolic and proteomic approach is implemented to study seed composition and seed-produced mucilage. The chia genome exhibits a significant expansion in mucilage synthesis genes (compared to Arabidopsis), and gene network analysis reveals potential regulators controlling seed mucilage production. Rosmarinic acid, a compound with enormous therapeutic potential, was classified as the most abundant polyphenol in seeds, and candidate genes for its complex pathway are described. Overall, this study provides important insights into the molecular basis for the unique characteristics of chia seeds.
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Affiliation(s)
- Gerardo Alejo-Jacuinde
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Héctor-Rogelio Nájera-González
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Ricardo A Chávez Montes
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Alfonso Carlos Barragán-Rosillo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Benjamin Perez Sanchez
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Damar López-Arredondo
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA
| | - Lenin Yong-Villalobos
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
| | - Luis Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto., 36821, Mexico.
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30
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Kaur N, Nayakoti S, Brock N, Halford NG. Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3395-3398. [PMID: 37369102 DOI: 10.1093/jxb/erad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This article comments on:
Kalinka A, Starczak M, Gackowski D, Stępień E, Achrem M. 2023. Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species. Journal of Experimental Botany 74, 3488–3502.
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Affiliation(s)
- Navneet Kaur
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - Natasha Brock
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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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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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: 9] [Impact Index Per Article: 9.0] [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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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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34
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Pisupati R, Nizhynska V, Mollá Morales A, Nordborg M. On the causes of gene-body methylation variation in Arabidopsis thaliana. PLoS Genet 2023; 19:e1010728. [PMID: 37141384 DOI: 10.1371/journal.pgen.1010728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/16/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Gene-body methylation (gbM) refers to sparse CG methylation of coding regions, which is especially prominent in evolutionarily conserved house-keeping genes. It is found in both plants and animals, but is directly and stably (epigenetically) inherited over multiple generations in the former. Studies in Arabidopsis thaliana have demonstrated that plants originating from different parts of the world exhibit genome-wide differences in gbM, which could reflect direct selection on gbM, but which could also reflect an epigenetic memory of ancestral genetic and/or environmental factors. Here we look for evidence of such factors in F2 plants resulting from a cross between a southern Swedish line with low gbM and a northern Swedish line with high gbM, grown at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we confirm that CG sites are either methylated (nearly 100% methylation across sampled cells) or unmethylated (approximately 0% methylation across sampled cells), and show that the higher level of gbM in the northern line is due to more sites being methylated. Furthermore, methylation variants almost always show Mendelian segregation, consistent with their being directly and stably inherited through meiosis. To explore how the differences between the parental lines could have arisen, we focused on somatic deviations from the inherited state, distinguishing between gains (relative to the inherited 0% methylation) and losses (relative to the inherited 100% methylation) at each site in the F2 generation. We demonstrate that deviations predominantly affect sites that differ between the parental lines, consistent with these sites being more mutable. Gains and losses behave very differently in terms of the genomic distribution, and are influenced by the local chromatin state. We find clear evidence for different trans-acting genetic polymorphism affecting gains and losses, with those affecting gains showing strong environmental interactions (G×E). Direct effects of the environment were minimal. In conclusion, we show that genetic and environmental factors can change gbM at a cellular level, and hypothesize that these factors can also lead to transgenerational differences between individuals via the inclusion of such changes in the zygote. If true, this could explain genographic pattern of gbM with selection, and would cast doubt on estimates of epimutation rates from inbred lines in constant environments.
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Affiliation(s)
- Rahul Pisupati
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Almudena Mollá Morales
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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Orantes-Bonilla M, Wang H, Lee HT, Golicz AA, Hu D, Li W, Zou J, Snowdon RJ. Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:113. [PMID: 37071201 PMCID: PMC10113308 DOI: 10.1007/s00122-023-04345-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/12/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Transcriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Huey Tyng Lee
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany
| | - Dandan Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenwen Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rod J Snowdon
- Department of Plant Breeding, Land Use and Nutrition, IFZ Research Centre for Biosystems, Justus Liebig University, Giessen, Germany.
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Hafner A, Mackenzie S. Re-analysis of publicly available methylomes using signal detection yields new information. Sci Rep 2023; 13:3307. [PMID: 36849495 PMCID: PMC9971211 DOI: 10.1038/s41598-023-30422-4] [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] [Received: 10/04/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023] Open
Abstract
Cytosine methylation is an epigenetic mark that participates in regulation of gene expression and chromatin stability in plants. Advancements in whole genome sequencing technologies have enabled investigation of methylome dynamics under different conditions. However, the computational methods for analyzing bisulfite sequence data have not been unified. Contention remains in the correlation of differentially methylated positions with the investigated treatment and exclusion of noise, inherent to these stochastic datasets. The prevalent approaches apply Fisher's exact test, logistic, or beta regression, followed by an arbitrary cut-off for differences in methylation levels. A different strategy, the MethylIT pipeline, utilizes signal detection to determine cut-off based on a fitted generalized gamma probability distribution of methylation divergence. Re-analysis of publicly available BS-seq data from two epigenetic studies in Arabidopsis and applying MethylIT revealed additional, previously unreported results. Methylome repatterning in response to phosphate starvation was confirmed to be tissue-specific and included phosphate assimilation genes in addition to sulfate metabolism genes not implicated in the original study. During seed germination plants undergo major methylome reprogramming and use of MethylIT allowed us to identify stage-specific gene networks. We surmise from these comparative studies that robust methylome experiments must account for data stochasticity to achieve meaningful functional analyses.
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Affiliation(s)
- Alenka Hafner
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA USA
| | - Sally Mackenzie
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA. .,Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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37
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Van Antro M, Prelovsek S, Ivanovic S, Gawehns F, Wagemaker NCAM, Mysara M, Horemans N, Vergeer P, Verhoeven KJF. DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures. Mol Ecol 2023; 32:428-443. [PMID: 36324253 PMCID: PMC10100429 DOI: 10.1111/mec.16757] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.
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Affiliation(s)
- Morgane Van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Stella Prelovsek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Slavica Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Mohamed Mysara
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Nele Horemans
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Philippine Vergeer
- Plant Ecology and Physiology, Radboud University, Nijmegen, The Netherlands.,Wageningen University and Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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38
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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