1
|
Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
Collapse
Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| |
Collapse
|
2
|
Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
Collapse
Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
3
|
Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
Collapse
Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
4
|
Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
Collapse
Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
| |
Collapse
|
5
|
Elakhdar A, Slaski JJ, Kubo T, Hamwieh A, Hernandez Ramirez G, Beattie AD, Capo-chichi LJ. Genome-wide association analysis provides insights into the genetic basis of photosynthetic responses to low-temperature stress in spring barley. FRONTIERS IN PLANT SCIENCE 2023; 14:1159016. [PMID: 37346141 PMCID: PMC10279893 DOI: 10.3389/fpls.2023.1159016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/04/2023] [Indexed: 06/23/2023]
Abstract
Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (FVFM, and FVF0) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.
Collapse
Affiliation(s)
- Ammar Elakhdar
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Jan J. Slaski
- Bio Industrial Services Division, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ludovic J.A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
6
|
Shi M, Wang C, Wang P, Zhang M, Liao W. Methylation in DNA, histone, and RNA during flowering under stress condition: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111431. [PMID: 36028071 DOI: 10.1016/j.plantsci.2022.111431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Flowering is the most critical transition period in the whole lifecycle of plants, and it is a highly sensitive period to stress. New combinations of temperature, drought stress, carbon dioxide and other abiotic/biotic conditions resulting from contemporary climate change affect the flowering process. Plants have evolved several strategies to deal with environmental stresses, including epigenetic modifications. Numerous studies show that environmental stresses trigger methylation/demethylation during flowering to preserve/accelerate plant lifecycle. What's more, histone and DNA methylation can be induced to respond to stresses, resulting in changes of flowering gene expression and enhancing stress tolerance in plants. Furthermore, RNA methylation may influence stress-regulated flowering by regulating mRNA stability and antioxidant mechanism. Our review presents the involvement of methylation in stress-repressed and stress-induced flowering. The crosstalk between methylation and small RNAs, phytohormones and exogenous substances (such as salicylic acid, nitric oxide) during flowering under different stresses were discussed. The latest regulatory evidence of RNA methylation in stress-regulated flowering was collected for the first time. Meanwhile, the limited evidences of methylation in biotic stress-induced flowering were summarized. Thus, the review provides insights into understanding of methylation mechanism in stress-regulated flowering and makes use for the development of regulating plant flowering at epigenetic level in the future.
Collapse
Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Meiling Zhang
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.
| |
Collapse
|
7
|
Rajpal VR, Rathore P, Mehta S, Wadhwa N, Yadav P, Berry E, Goel S, Bhat V, Raina SN. Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions. Front Cell Dev Biol 2022; 10:1020958. [PMID: 36340045 PMCID: PMC9628676 DOI: 10.3389/fcell.2022.1020958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
Collapse
Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | | | - Sahil Mehta
- School of Agricultural Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Eapsa Berry
- Maharishi Kanad Bhawan, Delhi School of Climate Change and Sustainability, University of Delhi, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Vishnu Bhat
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| |
Collapse
|
8
|
Galanti D, Ramos-Cruz D, Nunn A, Rodríguez-Arévalo I, Scheepens JF, Becker C, Bossdorf O. Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense. PLoS Genet 2022; 18:e1010452. [PMID: 36223399 PMCID: PMC9591053 DOI: 10.1371/journal.pgen.1010452] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/24/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being lower in colder regions and in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylated regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Collapse
Affiliation(s)
- Dario Galanti
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Daniela Ramos-Cruz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Leipzig, Germany
- Institute for Computer Science, University of Leipzig, Leipzig, Germany
| | - Isaac Rodríguez-Arévalo
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - J. F. Scheepens
- Plant Evolutionary Ecology, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
- * E-mail:
| |
Collapse
|
9
|
Wang M, He L, Chen B, Wang Y, Wang L, Zhou W, Zhang T, Cao L, Zhang P, Xie L, Zhang Q. Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810492. [PMID: 36142407 PMCID: PMC9504898 DOI: 10.3390/ijms231810492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.
Collapse
Affiliation(s)
- Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wei Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence:
| |
Collapse
|
10
|
Gong M, Huang T, Li Y, Li J, Tang L, Su E, Zou G, Bao D. Multi-Omics Analysis of Low-Temperature Fruiting Highlights the Promising Cultivation Application of the Nutrients Accumulation in Hypsizygus marmoreus. J Fungi (Basel) 2022; 8:jof8070695. [PMID: 35887452 PMCID: PMC9315786 DOI: 10.3390/jof8070695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
Hypsizygus marmoreus is a representative edible mushroom with low-temperature fruiting after a long postripening (LFLP). Clarifying the mechanism of LFLP and applying a rigorous low-temperature-limited process will optimize the mushroom cultivation process. This study performed an integrative multi-omics analysis of the molecular mechanism of LFLP in combination with genetic, physiological, and cultivation confirmation. The results showed that the amino acid content was increased during LFLP, mainly arginine. pH analysis showed acidification in the postripening stage and alkalization in the substrates of the reproductive growth stage. An enzyme activity test confirmed the increased enzyme activity of arginase and citrate synthase in the postripening stage. Weighted gene coexpression network analysis of the transcriptome and metabolomics indicated that pH variation is correlated mainly with changes in citrate and arginine. Multi-omics reveals a straightforward way of providing enriched materials for amino acid biosynthesis, namely, synergistically elevating citric acid and arginine through enhanced activity of the arginine synthesis branch pathway in the citrate cycle. Our study confirmed that GCN2 mediated metabolic adaptation by enhancing protein translation, highlighting its regulatory role during LFLP. Exogenously added citric acid and arginine shortened the postripening period by 10 days and increased the fruiting body yield by 10.2~15.5%. This research sheds light on the molecular mechanism of LFLP in H. marmoreus and highlights the promising application of nutrient accumulation in high-efficiency cultivation.
Collapse
Affiliation(s)
- Ming Gong
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (M.G.); (Y.L.); (L.T.)
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China;
| | - Tianyu Huang
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China;
| | - Yan Li
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (M.G.); (Y.L.); (L.T.)
| | - Jinxin Li
- Research and Development Center, Shanghai Finc Bio-Tech Inc., Shanghai 201401, China;
| | - Lihua Tang
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (M.G.); (Y.L.); (L.T.)
| | - Erzheng Su
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China;
| | - Gen Zou
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (M.G.); (Y.L.); (L.T.)
- Correspondence: (G.Z.); (D.B.)
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (M.G.); (Y.L.); (L.T.)
- Correspondence: (G.Z.); (D.B.)
| |
Collapse
|
11
|
Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
Collapse
Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| |
Collapse
|
12
|
Takehira K, Hayashi Y, Nozawa K, Chen L, Suzuki T, Masuta Y, Kato A, Ito H. DRD1, a SWI/SNF-like chromatin remodeling protein, regulates a heat-activated transposon in Arabidopsis thaliana. Genes Genet Syst 2021; 96:151-158. [PMID: 34373369 DOI: 10.1266/ggs.21-00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
ONSEN is a heat-activated LTR retrotransposon in Arabidopsis thaliana. Screens to identify transcriptional regulatory factors of ONSEN revealed a SWI/SNF-like chromatin remodeling protein, DRD1, which cooperates with plant-specific RNA polymerase and is involved in RNA-directed DNA methylation. ONSEN transcript level was increased in the drd1 mutant relative to wild-type under heat stress, indicating that DRD1 plays a significant role in the silencing of activated ONSEN under the stress condition. The transcript level of HsfA2, which is directly involved in transcriptional activation of ONSEN, was not higher in the drd1 mutant than in the wild-type. Interestingly, no transgenerational transposition of ONSEN was observed in the drd1 mutant, even though DNA methylation levels were significantly reduced and expression levels were increased compared to the wild-type. These results suggest that other factors are involved in the regulation of ONSEN transposition in addition to the transcript level of ONSEN.
Collapse
Affiliation(s)
| | - Yui Hayashi
- Graduate School of Life Science, Hokkaido University
| | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University
| | - Lu Chen
- Graduate School of Life Science, Hokkaido University
| | | | | | | | | |
Collapse
|
13
|
Li D, Feng BE, Liu YJ, Gong J, Tang YM, Zhang LP, Pang BS, Sun RW, Zhang FT, Chen ZB, Wang YB, Chen XC, Wang AP, Zhao CP, Gao SQ. Genome-wide identification and transcriptional characterization of DNA methyltransferases conferring temperature-sensitive male sterility in wheat. BMC Genomics 2021; 22:310. [PMID: 33926387 PMCID: PMC8082647 DOI: 10.1186/s12864-021-07600-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/11/2021] [Indexed: 01/18/2023] Open
Abstract
Background DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperature-sensitive genic male sterile (P/TGMS) lines play an important role in hybrid seed production of wheat. However, only a few studies have reported on the effect of DMT genes on temperature-sensitive male sterility of wheat. Although DMT genes have been investigated in some plant species, the identification and analysis of DMT genes in wheat (Triticum aestivum L.) based on genome-wide levels have not been reported. Results In this study, a detailed overview of phylogeny of 52 wheat DMT (TaDMT) genes was presented. Homoeolog retention for TaDMT genes was significantly above the average retention rate for whole-wheat genes, indicating the functional importance of many DMT homoeologs. We found that the strikingly high number of TaDMT genes resulted mainly from the significant expansion of the TaDRM subfamily. Intriguingly, all 5 paralogs belonged to the wheat DRM subfamily, and we speculated that tandem duplications might play a crucial role in the TaDRM subfamily expansion. Through the transcriptional analysis of TaDMT genes in a TGMS line BS366 and its hybrids with the other six fertile lines under sterile and fertile conditions, we concluded that TaCMT-D2, TaMET1-B1, and TaDRM-U6 might be involved in male sterility in BS366. Furthermore, a correlation analysis showed that TaMET1-B1 might negatively regulate the expression of TaRAFTIN1A, an important gene for pollen development, so we speculated regarding an epigenetic regulatory mechanism underlying the male sterility of BS366 via the interaction between TaMET1-B1 and TaRAFTIN1A. Conclusions Our findings presented a detailed phylogenic overview of the DMT genes and could provide novel insights into the effects of DMT genes on TGMS wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07600-7.
Collapse
Affiliation(s)
- Dan Li
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bian-E Feng
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,Shanxi Agricultural University, Taigu, 030800, China
| | - Yong-Jie Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jie Gong
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yi-Miao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Li-Ping Zhang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bin-Shuang Pang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ren-Wei Sun
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Feng-Ting Zhang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Zhao-Bo Chen
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yong-Bo Wang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xian-Chao Chen
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ai-Ping Wang
- Shanxi Agricultural University, Taigu, 030800, China.
| | - Chang-Ping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Shi-Qing Gao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
14
|
Meng H, Wang S, Yang W, Ding X, Li N, Chu Z, Li X. Identification of virulence associated milRNAs and their bidirectional targets in Rhizoctonia solani and maize during infection. BMC PLANT BIOLOGY 2021; 21:155. [PMID: 33771101 PMCID: PMC8004440 DOI: 10.1186/s12870-021-02930-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/10/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Anastomosis group 1 IA (AG1-IA) of Rhizoctonia solani is the major agent of banded leaf and sheath blight (BLSB) disease that causes severe yield loss in many worldwide crops. MicroRNAs (miRNAs) are ~ 22 nt non-coding RNAs that negatively regulate gene expression levels by mRNA degradation or translation inhibition. A better understanding of miRNA function during AG1-IA infection can expedite to elucidate the molecular mechanisms of fungi-host interactions. RESULTS In this study, we sequenced three small RNA libraries obtained from the mycelium of AG1-IA isolate, non-infected maize sheath and mixed maize sheath 3 days after inoculation. In total, 137 conserved and 34 novel microRNA-like small RNAs (milRNAs) were identified from the pathogen. Among these, one novel and 17 conserved milRNAs were identified as potential virulence-associated (VA) milRNAs. Subsequently, the prediction of target genes for these milRNAs was performed in both AG1-IA and maize, while functional annotation of these targets suggested a link to pathogenesis-related biological processes. Further, expression patterns of these virulence-associated milRNAs demonstrated that theyparticipate in the virulence of AG1-IA. Finally, regulation of one maize targeting gene, GRMZM2G412674 for Rhi-milRNA-9829-5p, was validated by dual-luciferase assay and identified to play a positive role in BLSB resistance in two maize mutants. These results suggest the global differentially expressed milRNAs of R. solani AG1-IA that participate in the regulation of target genes in both AG1-IA and maize to reinforce its pathogenicity. CONCLUSIONS Our data have provided a comprehensive overview of the VA-milRNAs of R. solani and identified that they are probably the virulence factors by directly interfered in host targeting genes. These results offer new insights on the molecular mechanisms of R.solani-maize interactions during the process of infection.
Collapse
Affiliation(s)
- Hongxu Meng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Shaoli Wang
- Yantai Academy of Agricultural Sciences, Yan'tai, 265500, Shandong, People's Republic of China
| | - Wei Yang
- Key Laboratory of Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Xinhua Ding
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Xiaoming Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| |
Collapse
|
15
|
Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae. G3-GENES GENOMES GENETICS 2020; 10:4387-4398. [PMID: 32988994 PMCID: PMC7718754 DOI: 10.1534/g3.120.401596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.
Collapse
|
16
|
Peng Z, Tian J, Luo R, Kang Y, Lu Y, Hu Y, Liu N, Zhang J, Cheng H, Niu S, Zhang J, Yao Y. MiR399d and epigenetic modification comodulate anthocyanin accumulation in Malus leaves suffering from phosphorus deficiency. PLANT, CELL & ENVIRONMENT 2020; 43:1148-1159. [PMID: 31833568 DOI: 10.1111/pce.13697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 05/14/2023]
Abstract
Inorganic phosphorus (Pi) deficiency induces anthocyanin accumulation in the leaves of some plant species; however, the molecular mechanisms underlying this phenomenon have not been well characterized. Here, we showed that microRNA399d (miR399d), high-affinity Pi transporter McPHT1;4, and McMYB10 are strongly induced in Malus leaves suffering from Pi deficiency. By culturing explants of transiently transformed plants in MS medium under conditions of Pi sufficiency and Pi deficiency, miR399d and McPHT1;4 were shown to play essential roles in the response to Pi deficiency and to play positive roles in the regulation of anthocyanin biosynthesis. Silencing of McHDA6 expression and treatment with the inhibitor trichostatin A suggested that the low expression of McHDA6 simultaneously reduced the transcription of McMET1 and decreased the methylation level of the McMYB10 promoter; however, the expression of McMYB10 and anthocyanin content were increased. Bimolecular fluorescence complementation and yeast two-hybrid assays revealed that McHDA6 binds directly to McMET1 through its BAH2 and DNMT1-RFD domains. Based on the results of our study, we propose a mechanism for the molecular regulation of anthocyanin biosynthesis, namely, the miR399d and epigenetic modification comodulation model, to explain the phenomenon in which leaves turn red under conditions of Pi deficiency.
Collapse
Affiliation(s)
- Zhen Peng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanhui Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanfen Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Na Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| |
Collapse
|
17
|
Perrone A, Martinelli F. Plant stress biology in epigenomic era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110376. [PMID: 32234231 DOI: 10.1016/j.plantsci.2019.110376] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanisms driving the capacity of plants to memorize a stress and to generate stress-resistant progenies are still unclear and scarcely investigated. The elucidation of these cryptic molecular switches will assist breeders in designing crops characterized by minimally compromised productivity in relation to stresses caused by climate change. The aim of this review is to briefly describe the most uptodate epigenomic approaches, update recent progresses in crop epigenomics in plant stress biology, and to stimulate the discussion of new epigenomic methods and approaches in the new era of "omic" sciences.
Collapse
Affiliation(s)
- Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy.
| | - Federico Martinelli
- Department of Biology, University of Firenze, Sesto Fiorentino, Florence, 50019, Italy.
| |
Collapse
|
18
|
DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species. Microorganisms 2020; 8:microorganisms8020296. [PMID: 32093408 PMCID: PMC7074839 DOI: 10.3390/microorganisms8020296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species.
Collapse
|
19
|
Guo X, Xie Q, Li B, Su H. Molecular characterization and transcription analysis of DNA methyltransferase genes in tomato (Solanum lycopersicum). Genet Mol Biol 2019; 43:e20180295. [PMID: 31429858 PMCID: PMC7197986 DOI: 10.1590/1678-4685-gmb-2018-0295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/08/2019] [Indexed: 11/22/2022] Open
Abstract
DNA methylation plays an important role in plant growth and development, gene expression regulation, and maintenance of genome stability. However, only little information regarding stress-related DNA methyltransferases (MTases) genes is available in tomato. Here, we report the analysis of nine tomato MTases, which were categorized into four known subfamilies. Structural analysis suggested their DNA methylase domains are highly conserved, whereas the N-terminals are divergent. Tissue-specific analysis of these MTase genes revealed that SlCMT2, SlCMT3, and SlDRM5 were expressed higher in young leaves, while SlMET1, SlCMT4, SlDRM7, and SlDRM8 were highly expressed in immature green fruit, and their expression declined continuously with further fruit development. In contrast, SlMETL was highly expressed in ripening fruit and displayed an up-regulated tendency during fruit development. In addition, the expression of SlMET1 in the ripening of mutant rin and Nr tomatoes is significantly higher compared to wild-type tomato, suggesting that SlMET1 was negatively regulated by the ethylene signal and ripening regulator MADS-RIN. Furthermore, expression analysis under abiotic stresses revealed that these MTase genes were stress-responsive and may function diversely in different stress conditions. Overall, our results provide valuable information for exploring the regulation of tomato fruit ripening and response to abiotic stress through DNA methylation.
Collapse
Affiliation(s)
- Xuhu Guo
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Qian Xie
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Baoyuan Li
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Huanzhen Su
- Shanxi Datong University, School of Life Sciences, Datong, China
| |
Collapse
|
20
|
Pandey N, Goswami N, Tripathi D, Rai KK, Rai SK, Singh S, Pandey-Rai S. Epigenetic control of UV-B-induced flavonoid accumulation in Artemisia annua L. PLANTA 2019; 249:497-514. [PMID: 30267151 DOI: 10.1007/s00425-018-3022-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/24/2018] [Indexed: 05/11/2023]
Abstract
UV-B-induced flavonoid biosynthesis is epigenetically regulated by site-specific demethylation of AaMYB1, AaMYC, and AaWRKY TF-binding sites inAaPAL1promoter-causing overexpression ofAaPALgene inArtemisia annua. The present study was undertaken to understand the epigenetic regulation of flavonoid biosynthesis under the influence of ultraviolet-B radiation using Artemisia annua L. as an experimental model. In-vitro propagated and acclimatized plantlets were treated with UV-B radiation (2.8 W m-2; 3 h), which resulted in enhanced accumulation of total flavonoid and phenolics content as well as eleven individual flavonoids measured through HPLC-DAC. Expression of eight genes (phenylanaline ammonia lyase, cinnamate-4-hydroxylase, 4-coumarate: CoA ligase; chalcone synthase, chalcone isomerase, cinnamoyl reductase, flavonoid-3'-hydroxylase, and flavones synthase) from upstream and downstream flavonoid biosynthetic pathways was measured through RT-PCR and RT-Q-PCR and all were variably induced under UV-B irradiation. Among them, AaPAL1 transcript and its protein were most significantly upregulated. Global DNA methylation analysis revealed hypomethylation of genomic DNA in A. annua. Further epigenetic characterization of promoter region of AaPAL1 revealed cytosine demethylation at five sites, which in turn caused epigenetic activation of six transcription factor-binding sites including QELEMENT, EBOXBNNAPA/MYCCONSENSUSAT, MYBCORE, MYBCOREATCYCB1, and GCCCORE. MYB transcription factors are positive regulators of flavonoid biosynthesis. Epigenetic activation of transcription-enhancing cis-regulatory elements in AaPAL1 promoter and subsequent overexpression of AaMYB1 and AaMYC and AaWRKY transcription factors under UV-B irradiation may probably be the reason for higher AaPAL1 expression and hence greater biosynthesis of flavonoids in A. annua L. The present study is the first report that provides mechanistic evidence of epigenetic regulation of flavonoid biosynthesis under UV-B radiation in A. annua L.
Collapse
Affiliation(s)
- Neha Pandey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Department of Botany, CMP Degree College, University of Allahabad, Allahabad, India
| | - Niraj Goswami
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepika Tripathi
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Krishna Kumar Rai
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sanjay Kumar Rai
- Department of Horticulture, Dr. Rajendra Prasad Agricultural University, Pusa, Samastipur, Bihar, India
| | - Shilpi Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Shashi Pandey-Rai
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India.
| |
Collapse
|
21
|
Mousavi S, Regni L, Bocchini M, Mariotti R, Cultrera NGM, Mancuso S, Googlani J, Chakerolhosseini MR, Guerrero C, Albertini E, Baldoni L, Proietti P. Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress. Sci Rep 2019; 9:1093. [PMID: 30705308 PMCID: PMC6355907 DOI: 10.1038/s41598-018-37496-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Cultivated olive, a typical fruit crop species of the semi-arid regions, could successfully face the new scenarios driven by the climate change through the selection of tolerant varieties to salt and drought stresses. In the present work, multidisciplinary approaches, including physiological, epigenetic and genetic studies, have been applied to clarify the salt tolerance mechanisms in olive. Four varieties (Koroneiki, Royal de Cazorla, Arbequina and Picual) and a related form (O. europaea subsp. cuspidata) were grown in a hydroponic system under different salt concentrations from zero to 200 mM. In order to verify the plant response under salt stress, photosynthesis, gas exchange and relative water content were measured at different time points, whereas chlorophyll and leaf concentration of Na+, K+ and Ca2+ ions, were quantified at 43 and 60 days after treatment, when stress symptoms became prominent. Methylation sensitive amplification polymorphism (MSAP) technique was used to assess the effects of salt stress on plant DNA methylation. Several fragments resulted differentially methylated among genotypes, treatments and time points. Real time quantitative PCR (RT-qPCR) analysis revealed significant expression changes related to plant response to salinity. Four genes (OePIP1.1, OePetD, OePI4Kg4 and OeXyla) were identified, as well as multiple retrotransposon elements usually targeted by methylation under stress conditions.
Collapse
Affiliation(s)
- Soraya Mousavi
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy
| | - Luca Regni
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Marika Bocchini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | | | | | - Stefano Mancuso
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | - Jalaladdin Googlani
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | | | | | - Emidio Albertini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy.
| | - Primo Proietti
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| |
Collapse
|
22
|
Avila LM, Obeidat W, Earl H, Niu X, Hargreaves W, Lukens L. Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure. BMC Genomics 2018; 19:761. [PMID: 30342485 PMCID: PMC6196024 DOI: 10.1186/s12864-018-5134-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their alleviation are shared or vary across genotypes. In this study we identify individual transcripts and groups of functionally related transcripts that consistently respond to cold and its alleviation. Genes that respond differently to temperature changes across genotypes may have limited functional importance. We investigate if these genes share functions, and if their genotype-specific gene expression levels change in magnitude or rank across temperatures. RESULTS We estimate transcript abundances from over 22,000 genes in two unrelated Zea mays inbred lines during and after cold temperature exposure. Genotype and temperature contribute to many genes' abundances. Past cold exposure affects many fewer genes. Genes up-regulated in cold encode many cytokinin glucoside biosynthesis enzymes, transcription factors, signalling molecules, and proteins involved in diverse environmental responses. After cold exposure, protease inhibitors and cuticular wax genes are newly up-regulated, and environmentally responsive genes continue to be up-regulated. Genes down-regulated in response to cold include many photosynthesis, translation, and DNA replication associated genes. After cold exposure, DNA replication and translation genes are still preferentially downregulated. Lignin and suberin biosynthesis are newly down-regulated. DNA replication, reactive oxygen species response, and anthocyanin biosynthesis genes have strong, genotype-specific temperature responses. The ranks of genotypes' transcript abundances often change across temperatures. CONCLUSIONS We report a large, core transcriptome response to cold and the alleviation of cold. In cold, many of the core suite of genes are up or downregulated to control plant growth and photosynthesis and limit cellular damage. In recovery, core responses are in part to prepare for future stress. Functionally related genes are consistently and greatly up-regulated in a single genotype in response to cold or its alleviation, suggesting positive selection has driven genotype-specific temperature responses in maize.
Collapse
Affiliation(s)
- Luis M Avila
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Wisam Obeidat
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Hugh Earl
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Xiaomu Niu
- Dupont/Pioneer, 7300 NW 62nd Ave, DuPont Pioneer, Johnston, Iowa, 50131 USA
| | - William Hargreaves
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1 Canada
| |
Collapse
|
23
|
Uthup TK, Karumamkandathil R, Ravindran M, Saha T. Heterografting induced DNA methylation polymorphisms in Hevea brasiliensis. PLANTA 2018; 248:579-589. [PMID: 29799082 DOI: 10.1007/s00425-018-2918-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/11/2018] [Indexed: 05/19/2023]
Abstract
Heterografting induced intraclonal epigenetic variations were detected among rubber plants. Interaction between genetically divergent root stock and scion tissues might have triggered these epigenetic changes which may eventually lead to intraclonal variability in rubber. DNA methylation in response to stress may be associated with the alteration in gene transcription leading to morphological changes in plants. Rubber tree is commercially propagated by bud grafting where the scion of a high yielding variety is grafted on to a genetically divergent root stock. Still, significant levels of intraclonal variations exist among them. Epigenetic changes associated with heterografting may be partly responsible for this conundrum. In the present study, an attempt was made to identify the impact of divergent root stock on the epigenome of scion in grafted rubber plants. Heterografts were developed by grafting eye buds from a single polyembryony derived seedling on to genetically divergent root stocks of unknown parentage. The plants were uniformly maintained and their DNA was subjected to MSAP analysis. Polymorphic DNA methylation bands corresponding to CG as well as the plant-specific CHG types of methylation were observed. Cloning of selected polymorphic regions and bisulfite sequencing confirmed the presence of methylation in the promoter and coding region of important genes including an LRR receptor kinase gene. Since divergent root stock is the major factor differentiating the grafted plants, the changes in DNA methylation patterns might have been triggered by the interaction between the two genetically different tissues of stock and scion. The study assumes importance in Hevea, because accumulation and maintenance of epigenetic changes in functional genes and promoters during subsequent cycles of vegetative propagation may contribute towards intraclonal variability eventually leading to altered phenotypes.
Collapse
Affiliation(s)
- Thomas K Uthup
- Advanced Centre for Molecular Biology and Biotechnology, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala, 686009, India.
| | - Rekha Karumamkandathil
- Advanced Centre for Molecular Biology and Biotechnology, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala, 686009, India
| | - Minimol Ravindran
- Advanced Centre for Molecular Biology and Biotechnology, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala, 686009, India
| | - Thakurdas Saha
- Advanced Centre for Molecular Biology and Biotechnology, Rubber Research Institute of India, Rubber Board P O, Kottayam, Kerala, 686009, India
| |
Collapse
|
24
|
Dynamic DNA Methylation in Plant Growth and Development. Int J Mol Sci 2018; 19:ijms19072144. [PMID: 30041459 PMCID: PMC6073778 DOI: 10.3390/ijms19072144] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/12/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification required for transposable element (TE) silencing, genome stability, and genomic imprinting. Although DNA methylation has been intensively studied, the dynamic nature of methylation among different species has just begun to be understood. Here we summarize the recent progress in research on the wide variation of DNA methylation in different plants, organs, tissues, and cells; dynamic changes of methylation are also reported during plant growth and development as well as changes in response to environmental stresses. Overall DNA methylation is quite diverse among species, and it occurs in CG, CHG, and CHH (H = A, C, or T) contexts of genes and TEs in angiosperms. Moderately expressed genes are most likely methylated in gene bodies. Methylation levels decrease significantly just upstream of the transcription start site and around transcription termination sites; its levels in the promoter are inversely correlated with the expression of some genes in plants. Methylation can be altered by different environmental stimuli such as pathogens and abiotic stresses. It is likely that methylation existed in the common eukaryotic ancestor before fungi, plants and animals diverged during evolution. In summary, DNA methylation patterns in angiosperms are complex, dynamic, and an integral part of genome diversity after millions of years of evolution.
Collapse
|
25
|
Single-base resolution methylome analysis shows epigenetic changes in Arabidopsis seedlings exposed to microgravity spaceflight conditions on board the SJ-10 recoverable satellite. NPJ Microgravity 2018; 4:12. [PMID: 30038957 PMCID: PMC6043569 DOI: 10.1038/s41526-018-0046-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/28/2018] [Accepted: 06/01/2018] [Indexed: 01/25/2023] Open
Abstract
DNA methylation is a very important epigenetic modification that participates in many biological functions. Although many studies of DNA methylation have been reported in various plant species, few studies have assessed the global DNA methylation pattern in plants challenged by exposure to microgravity conditions. In this report, we mapped the Arabidopsis genome methylation pattern changes associated with microgravity conditions on board the Chinese recoverable scientific satellite SJ-10 at single-base resolution. Interestingly, we found epigenetic differences in Arabidopsis seedlings exposed to microgravity in that the Arabidopsis genome exhibits lower methylation levels in the CHG, CHH, and CpG contexts under microgravity conditions. Microgravity stimulation was related to altered methylation of a number of genes, including DNA methylation-associated genes, hormone signaling related genes, cell-wall modification genes and transposable elements (TEs). Relatively unstable DNA methylation of TEs was responsible for the induction of active transposons. These observations suggest that DNA demethylation within TEs may affect the transcription of transposons in response to microgravity conditions. In summary, the results of this investigation are beneficial for understanding the mechanism of plant adaptation to microgravity and improve strategies to allow plants to adapt to space. Spaceflight alters the pattern of chemical tags that adorn DNA in plant seedlings. Weiming Cai and colleagues from the Shanghai Institute of Plant Physiology and Ecology, China, profiled the genome-wide epigenetic patterns of Arabidopsis thaliana seedlings that spent 60 h in the microgravity of low Earth orbit aboard the Shijian-10 recoverable satellite. They analyzed the distribution of methyl tags across the genome — an epigenetic mark that affects gene expression levels — and found that seedlings exposed to microgravity had lower methylation on average than control plants grown on the ground, although certain genes related to methylation, transcription factors and hormones tended to be more methylated. Epigenetic differences were also observed among genes involved in cell-wall modification and in transposable elements. The findings could help inform the design of plants optimized for growth in space.
Collapse
|
26
|
Masuta Y, Kawabe A, Nozawa K, Naito K, Kato A, Ito H. Characterization of a heat-activated retrotransposon in Vigna angularis. BREEDING SCIENCE 2018; 68:168-176. [PMID: 29875600 PMCID: PMC5982181 DOI: 10.1270/jsbbs.17085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 05/14/2023]
Abstract
In plants, several transposable elements are conserved across species. We found a homolog of ONSEN, which is a heat-activated retrotransposon originally isolated from Arabidopsis thaliana, in Vigna. The ONSEN-like elements (VaONS) were detected in all the analyzed Japanese accessions of Vigna angularis (adzuki bean) by Southern blot analysis. However, VaONS sequences were observed to be polymorphic in the different accessions. Interestingly, extrachromosomal DNA (ecDNA) was detected in some accessions of adzuki bean, indicating the conserved heat-activation of VaONS. Furthermore, we successfully induced retrotransposition of VaONS in adzuki plant regenerated through callus. Findings of our study should provide a new tool for molecular breeding of adzuki bean.
Collapse
Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo Motoyama, Kita-ku, Kyoto 603-8555,
Japan
| | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization,
2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
27
|
Sudan J, Raina M, Singh R. Plant epigenetic mechanisms: role in abiotic stress and their generational heritability. 3 Biotech 2018; 8:172. [PMID: 29556426 PMCID: PMC5845050 DOI: 10.1007/s13205-018-1202-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/07/2018] [Indexed: 10/17/2022] Open
Abstract
Plants have evolved various defense mechanisms including morphological adaptations, cellular pathways, specific signalling molecules and inherent immunity to endure various abiotic stresses during different growth stages. Most of the defense mechanisms are controlled by stress-responsive genes by transcribing and translating specific genes. However, certain modifications of DNA and chromatin along with small RNA-based mechanisms have also been reported to regulate the expression of stress-responsive genes and constitute another line of defense for plants in their struggle against stresses. More recently, studies have suggested that these modifications are heritable to the future generations as well, thereby indicating their possible role in the evolutionary mechanisms related to abiotic stresses.
Collapse
Affiliation(s)
- Jebi Sudan
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu and Kashmir India
| | - Meenakshi Raina
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu and Kashmir India
| | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu and Kashmir India
| |
Collapse
|
28
|
Xu J, Zhou S, Gong X, Song Y, van Nocker S, Ma F, Guan Q. Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:672-687. [PMID: 28796917 PMCID: PMC5787839 DOI: 10.1111/pbi.12820] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/12/2017] [Accepted: 08/07/2017] [Indexed: 05/11/2023]
Abstract
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analysed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analysed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars. We found that the apple genome exhibits ~54%, ~38% and ~8.5% methylation at CG, CHG and CHH sequence contexts, respectively. We additionally documented changes in gene expression associated with water deficit in an attempt to link methylation and gene expression changes. Global methylation and transcription analysis revealed that promoter-unmethylated genes showed higher expression levels than promoter-methylated genes. Gene body methylation appears to be positively correlated with gene expression. Water deficit stress was associated with changes in methylation at a multitude of genes, including those encoding transcription factors (TFs) and transposable elements (TEs). These results present a methylome map of the apple genome and reveal widespread DNA methylation alterations in response to water deficit stress. These data will be helpful for understanding potential linkages between DNA methylation and gene expression in plants growing in natural environments and challenged with abiotic and biotic stresses.
Collapse
Affiliation(s)
- Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Shasha Zhou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Yi Song
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Steve van Nocker
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| |
Collapse
|
29
|
Wang J, Meng X, Dobrovolskaya OB, Orlov YL, Chen M. Non-coding RNAs and Their Roles in Stress Response in Plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:301-312. [PMID: 29017967 PMCID: PMC5673675 DOI: 10.1016/j.gpb.2017.01.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/04/2017] [Accepted: 01/26/2017] [Indexed: 02/04/2023]
Abstract
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.
Collapse
Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianwen Meng
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Oxana B Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
30
|
Masuda S, Nozawa K, Matsunaga W, Masuta Y, Kawabe A, Kato A, Ito H. Characterization of a heat-activated retrotransposon in natural accessions of Arabidopsis thaliana. Genes Genet Syst 2017; 91:293-299. [PMID: 27980240 DOI: 10.1266/ggs.16-00045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Natural accessions are used for studying intraspecies genetic variation in the model plant Arabidopsis thaliana in order to address fundamental questions of evolution. Transposable elements are responsible for a wide range of mutations and play significant roles in shaping a genome over evolutionary time. In the present study, we aimed to characterize ONSEN, a heat-activated long terminal repeat (LTR) retrotransposon, in natural A. thaliana accessions. Southern blot analysis demonstrated that ONSEN was present in all the studied accessions, but the copy number was diverse. Olympia-1 contained a single ONSEN copy, located in the centromere of Chromosome 3. A premature stop codon in Olympia-1 ONSEN presumably abolishes integrase activity, which in turn presumably renders the retrotransposon non-functional. Hybridization of Col-0 with Olympia-1 showed that several ONSEN copies in Col-0 were activated by heat stress and maintained their transpositional activity in the progeny.
Collapse
Affiliation(s)
| | | | | | | | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University
| | | | | |
Collapse
|
31
|
Pandey G, Yadav CB, Sahu PP, Muthamilarasan M, Prasad M. Salinity induced differential methylation patterns in contrasting cultivars of foxtail millet (Setaria italica L.). PLANT CELL REPORTS 2017; 36:759-772. [PMID: 27999979 DOI: 10.1007/s00299-016-2093-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/07/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide methylation analysis of foxtail millet cultivars contrastingly differing in salinity tolerance revealed DNA demethylation events occurring in tolerant cultivar under salinity stress, eventually modulating the expression of stress-responsive genes. Reduced productivity and significant yield loss are the adverse effects of environmental conditions on physiological and biochemical pathways in crop plants. In this context, understanding the epigenetic machinery underlying the tolerance traits in a naturally stress tolerant crop is imperative. Foxtail millet (Setaria italica) is known for its better tolerance to abiotic stresses compared to other cereal crops. In the present study, methylation-sensitive amplified polymorphism (MSAP) technique was used to quantify the salt-induced methylation changes in two foxtail millet cultivars contrastingly differing in their tolerance levels to salt stress. The study highlighted that the DNA methylation level was significantly reduced in tolerant cultivar compared to sensitive cultivar. A total of 86 polymorphic MSAP fragments were identified, sequenced and functionally annotated. These fragments showed sequence similarity to several genes including ABC transporter, WRKY transcription factor, serine threonine-protein phosphatase, disease resistance, oxidoreductases, cell wall-related enzymes and retrotransposon and transposase like proteins, suggesting salt stress-induced methylation in these genes. Among these, four genes were chosen for expression profiling which showed differential expression pattern between both cultivars of foxtail millet. Altogether, the study infers that salinity stress induces genome-wide DNA demethylation, which in turn, modulates expression of corresponding genes.
Collapse
Affiliation(s)
- Garima Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Chandra Bhan Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Pranav Pankaj Sahu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India.
| |
Collapse
|
32
|
|
33
|
Han B, Li W, Chen Z, Xu Q, Luo J, Shi Y, Li X, Yan X, Zhang J. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure. PLoS One 2016; 11:e0160358. [PMID: 27494266 PMCID: PMC4975392 DOI: 10.1371/journal.pone.0160358] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 07/18/2016] [Indexed: 01/25/2023] Open
Abstract
DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.
Collapse
Affiliation(s)
- Bingshe Han
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Zuozhou Chen
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qiongqiong Xu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Juntao Luo
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yingdi Shi
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaoxia Li
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaonan Yan
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
| | - Junfang Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University, Shanghai, China
- * E-mail:
| |
Collapse
|
34
|
Paredes U, Radersma R, Cannell N, While GM, Uller T. Low Incubation Temperature Induces DNA Hypomethylation in Lizard Brains. ACTA ACUST UNITED AC 2016; 325:390-5. [PMID: 27328739 DOI: 10.1002/jez.2024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 02/04/2023]
Abstract
Developmental stress can have organizational effects on suites of physiological, morphological, and behavioral characteristics. In lizards, incubation temperature is perhaps the most significant environmental variable affecting embryonic development. Wall lizards (Podarcis muralis) recently introduced by humans from Italy to England experience stressfully cool incubation conditions, which we here show reduce growth and increase the incidence of scale malformations. Using a methylation-sensitive AFLP protocol optimized for vertebrates, we demonstrate that this low incubation temperature also causes hypomethylation of DNA in brain tissue. A consistent pattern across methylation-susceptible AFLP loci suggests that hypomethylation is a general response and not limited to certain CpG sites. The functional consequences of hypomethylation are unknown, but it could contribute to genome stability and regulation of gene expression. Further studies of the effects of incubation temperature on DNA methylation in ectotherm vertebrates may reveal mechanisms that explain why the embryonic thermal environment often has physiological and behavioral consequences for offspring.
Collapse
Affiliation(s)
- Ursula Paredes
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Reinder Radersma
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Naomi Cannell
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Geoffrey M While
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,School of Biological Sciences, University of Tasmania, Tasmania, Australia
| | - Tobias Uller
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
35
|
Chen Y, Müller F, Rieu I, Winter P. Epigenetic events in plant male germ cell heat stress responses. PLANT REPRODUCTION 2016; 29:21-29. [PMID: 26639000 DOI: 10.1007/s00497-015-0271-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
A review on pollen epigenetics. Plants grow in an ever-changing environment and are used to environmental fluctuations such as high and low temperatures during their life cycles. To cope with adverse conditions, plants have evolved intricate short-term and long-term mechanisms to respond and adapt to external stresses. The plant's ability to respond to stresses largely depends on its capacity to modulate the transcriptome rapidly and specifically. Epigenetic mechanisms, including DNA methylation, chromatin dynamics and small RNAs, play an essential role in the regulation of stress-responsive gene expression. Stress-related covalent modifications of DNA and histones can be passed on during mitosis and meiosis to the next generation and provide a memory that enables the plant and even its offspring to adopt better to a subsequent stress. Plant reproduction, in particular pollen development, is the most stress-sensitive process in the life cycle of the organism. In particular, developmental stages around the meiotic and mitotic divisions are the most vulnerable. In this review, we highlight the current understanding of epigenetic mechanisms involved in pollen development and speculate on their roles in pollen heat stress response.
Collapse
Affiliation(s)
| | - Florian Müller
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Ivo Rieu
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | | |
Collapse
|
36
|
Elhamamsy AR. DNA methylation dynamics in plants and mammals: overview of regulation and dysregulation. Cell Biochem Funct 2016; 34:289-98. [PMID: 27003927 DOI: 10.1002/cbf.3183] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
DNA methylation is a major epigenetic marking mechanism regulating various biological functions in mammals and plant. The crucial role of DNA methylation has been observed in cellular differentiation, embryogenesis, genomic imprinting and X-chromosome inactivation. Furthermore, DNA methylation takes part in disease susceptibility, responses to environmental stimuli and the biodiversity of natural populations. In plant, different types of environmental stress have demonstrated the ability to alter the archetype of DNA methylation through the genome, change gene expression and confer a mechanism of adaptation. DNA methylation dynamics are regulated by three processes de novo DNA methylation, methylation maintenance and DNA demethylation. These processes have their similarities and differences between mammals and plants. Furthermore, the dysregulation of DNA methylation dynamics represents one of the primary molecular mechanisms of developing diseases in mammals. This review discusses the regulation and dysregulation of DNA methylation in plants and mammals. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Amr Rafat Elhamamsy
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| |
Collapse
|
37
|
A Stress-Activated Transposon in Arabidopsis Induces Transgenerational Abscisic Acid Insensitivity. Sci Rep 2016; 6:23181. [PMID: 26976262 PMCID: PMC4791638 DOI: 10.1038/srep23181] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/25/2016] [Indexed: 01/05/2023] Open
Abstract
Transposable elements (TEs), or transposons, play an important role in adaptation. TE insertion can affect host gene function and provides a mechanism for rapid increases in genetic diversity, particularly because many TEs respond to environmental stress. In the current study, we show that the transposition of a heat-activated retrotransposon, ONSEN, generated a mutation in an abscisic acid (ABA) responsive gene, resulting in an ABA-insensitive phenotype in Arabidopsis, suggesting stress tolerance. Our results provide direct evidence that a transposon activated by environmental stress could alter the genome in a potentially positive manner. Furthermore, the ABA-insensitive phenotype was inherited when the transcription was disrupted by an ONSEN insertion, whereas ABA sensitivity was recovered when the effects of ONSEN were masked by IBM2. These results suggest that epigenetic mechanisms in host plants typically buffered the effect of a new insertion, but could selectively “turn on” TEs when stressed.
Collapse
|
38
|
Xin C, Hou R, Wu F, Zhao Y, Xiao H, Si W, Ali ME, Cai L, Guo J. Analysis of cytosine methylation status in potato by methylation-sensitive amplified polymorphisms under low-temperature stress. JOURNAL OF PLANT BIOLOGY 2015; 58:383-390. [DOI: 10.1007/s12374-015-0316-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
|
39
|
Pandey N, Pandey-Rai S. Deciphering UV-B-induced variation in DNA methylation pattern and its influence on regulation of DBR2 expression in Artemisia annua L. PLANTA 2015; 242:869-879. [PMID: 25998525 DOI: 10.1007/s00425-015-2323-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/03/2015] [Indexed: 06/04/2023]
Abstract
UV-B-caused DNA hypomethylation and UV-B-mediated epigenetic activation of additional WRKY-binding site(s) in the DBR2 promoter may contribute to the overexpression of the DBR2 gene in Artemisia annua. DNA methylation is one of the key mechanisms behind stress-induced transcriptional switch off/on. Here, we evaluate the DNA methylation level in response to UV-B radiation in Artemisia annua which produces artemisinin, a sesquiterpene that has been recommended by WHO for the frontline treatment of malaria. However, the drug is facing serious shortage due to its low concentration in plants. UV-B treatment (3 h) enhanced artemisinin concentration up to 1.91-fold as compared to control. A key regulatory gene of artemisinin biosynthesis, DBR2 was upregulated under UV-B. This study presents observations regarding contributions of DNA methylation to the gene regulation using DBR2 as an example. Restriction digestion of genomic DNA by isoschizomers (MspI and HpaII) suggested UV-B involvement in DNA hypomethylation in A. annua. The global level of DNA methylation (R) was 3.4 and 5.9% for UV-B treated and control plants, respectively, attesting hypomethylation of DNA in response to UV-B. Further bisulfite sequencing PCR showed demethylation at two CHG sites in 18S rRNA gene. Similarly, bisulfite sequencing of promoter region of DBR2 has demonstrated demethylation at 4 CG-, 4 CHH- and 2 CHG-sites. In silico analysis revealed UV-B-mediated demethylation at seven putative transcription factor binding sites including WRKY, which are positive regulators of artemisinin biosynthesis. UV-B treatment has resulted in activation of additional WRKY-binding site in UV-B-treated plants compared with single active WRKY-binding site in control and this could be the probable reason for overexpression of DBR2. It is suggested that DNA demethylation is an important epigenetic response to UV-B radiation in A. annua that surely will provide new horizons to further elucidate the mechanistic evidence of plant's responses to UV-B radiation.
Collapse
Affiliation(s)
- Neha Pandey
- Laboratory of Morphogenesis, Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | | |
Collapse
|
40
|
Sun P, Mao Y, Li G, Cao M, Kong F, Wang L, Bi G. Comparative transcriptome profiling of Pyropia yezoensis (Ueda) M.S. Hwang & H.G. Choi in response to temperature stresses. BMC Genomics 2015; 16:463. [PMID: 26081586 PMCID: PMC4470342 DOI: 10.1186/s12864-015-1586-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 04/27/2015] [Indexed: 12/20/2022] Open
Abstract
Background Pyropia yezoensis is a model organism often used to investigate the mechanisms underlying stress tolerance in intertidal zones. The digital gene expression (DGE) approach was used to characterize a genome-wide comparative analysis of differentially expressed genes (DEGs) that influence the physiological, developmental or biochemical processes in samples subjected to 4 treatments: high-temperature stress (HT), chilling stress (CS), freezing stress (FS) and normal temperature (NT). Results Equal amounts of total RNAs collected from 8 samples (two biological replicates per treatment) were sequenced using the Illumina/Solexa platform. Compared with NT, a total of 2202, 1334 and 592 differentially expressed unigenes were detected in HT, CS and FS respectively. Clustering analysis suggested P. yezoensis acclimates to low and high-temperature stress condition using different mechanisms: In heat stress, the unigenes related to replication and repair of DNA and protein processing in endoplasmic reticulum were active; however at low temperature stresses, unigenes related to carbohydrate metabolism and energy metabolism were active. Analysis of gene differential expression showed that four categories of DEGs functioning as temperature sensors were found, including heat shock proteins, H2A, histone deacetylase complex and transcription factors. Heat stress caused chloroplast genes down-regulated and unigenes encoding metacaspases up-regulated, which is an important regulator of PCD. Cold stress caused an increase in the expression of FAD to improve the proportion of polyunsaturated fatty acids. An up-regulated unigene encoding farnesyl pyrophosphate synthase was found in cold stress, indicating that the plant hormone ABA also played an important role in responding to temperature stress in P. yezoensis. Conclusion The variation of amount of unigenes and different gene expression pattern under different temperature stresses indicated the complicated and diverse regulation mechanism in response to temperature stress in P. yezoensis. Several common metabolism pathways were found both in P. yezoensis and in higher plants, such as FAD in low-temperature stress and HSP in heat stress. Meanwhile, many chloroplast genes and unigene related to the synthesis of abscisic acid were detected, revealing its unique temperature-regulation mechanism in this intertidal species. This sequencing dataset and analysis may serve as a valuable resource to study the mechanisms involved in abiotic stress tolerance in intertidal seaweeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1586-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Peipei Sun
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Guiyang Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Min Cao
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Li Wang
- Institute of Plant Resources, Dalian Nationalities University, Dalian, 116600, China.
| | - Guiqi Bi
- Key Laboratory of Marine Genetics and Breeding (MOE), College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
41
|
Tulpan D, Leger S, Tchagang A, Pan Y. Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. BMC Genomics 2015; 16:299. [PMID: 25887590 PMCID: PMC4426649 DOI: 10.1186/s12864-015-1496-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/27/2015] [Indexed: 11/12/2022] Open
Abstract
Background While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gene annotations that can be used as potential starting points for wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein correspondences are provided. Results DNA and protein sequences and corresponding annotations for T. aestivum and 9 other plant species were collected from Ensembl Plants release 22 and curated. Cliques of predicted 1-to-1 orthologs were identified and an annotation enrichment model was defined based on existing gene-GO term associations and phylogenetic relationships among wheat and 9 other plant species. A total of 13 cliques of size 10 were identified, which represent putative functionally equivalent genes and proteins in the 10 plant species. Eighty-five new and more specific GO terms were associated with wheat genes in the 13 cliques of size 10, which represent a 65% increase compared with the previously 130 known GO terms. Similar expression patterns for 4 genes from Arabidopsis, barley, maize and rice in cliques of size 10 provide experimental evidence to support our model. Overall, based on clique size equal or larger than 3, our model enriched the existing gene-GO term associations for 7,838 (8%) wheat genes, of which 2,139 had no previous annotation. Conclusions Our novel comparative genomics approach enriches existing T. aestivum gene annotations based on cliques of predicted 1-to-1 orthologs, phylogenetic relationships and existing gene ontologies from 9 other plant species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1496-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dan Tulpan
- Information and Communications Technologies, National Research Council Canada, Moncton, New Brunswick, E1A 7R1, Canada.
| | - Serge Leger
- Information and Communications Technologies, National Research Council Canada, Moncton, New Brunswick, E1A 7R1, Canada.
| | - Alain Tchagang
- Information and Communications Technologies, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada.
| | - Youlian Pan
- Information and Communications Technologies, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada.
| |
Collapse
|
42
|
Naydenov M, Baev V, Apostolova E, Gospodinova N, Sablok G, Gozmanova M, Yahubyan G. High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 87:102-8. [PMID: 25576840 DOI: 10.1016/j.plaphy.2014.12.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/31/2014] [Indexed: 05/20/2023]
Abstract
Along with its essential role in the maintenance of genome integrity, DNA methylation takes part in regulation of genes which are important for plant development and stress response. In plants, DNA methylation process can be directed by small RNAs in process known as RNA-directed DNA methylation (RdDM) involving two plant-specific RNA polymerases - PolIV and PolV. The aim of the present study was to investigate the effect of heat stress on the expression of genes encoding key players in DNA methylation - DNA methyltransferase (MET1, CMT3, and DRM2), the largest subunits of PoIIV and PolV (NRPD1 and NRPE1 respectively) and the DNA demethylase ROS1. We also examined the high-temperature effect on two protein-coding genes - At3g50770 and At5g43260 whose promoters contain transposon insertions and are affected by DNA-methylation, as well as on the AtSN1, a SINE-like retrotransposon. To assess the involvement of PolIV and PolV in heat stress response, the promoter methylation status and transcript levels of these genes were compared between wild type and double mutant lacking NRPD1 and NRPE1. The results demonstrate coordinated up-regulation of the DRM2, NRPD1 and NRPE1 in response to high temperature and suggest that PolIV and/or PolV might be required for the induction of DRM2 expression under heat stress. The ROS1 expression was confirmed to be suppressed in the mutant lacking active PolIV and PolV that might be a consequence of abolished DNA methylation. The increased expression of At3g50770 in response to elevated temperature correlated with reduced promoter DNA methylation, while the stress response of At5g43260 did not show inverse correlation between promoter methylation and gene expression. Our results also imply that PolIV and/or PolV could regulate gene expression under stress conditions not only through RdDM but also by acting in other regulatory processes.
Collapse
Affiliation(s)
- Mladen Naydenov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Nadezhda Gospodinova
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, San Michele 38010, Italy
| | - Mariyana Gozmanova
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
| |
Collapse
|
43
|
Bocchini M, Bartucca ML, Ciancaleoni S, Mimmo T, Cesco S, Pii Y, Albertini E, Del Buono D. Iron deficiency in barley plants: phytosiderophore release, iron translocation, and DNA methylation. FRONTIERS IN PLANT SCIENCE 2015; 6:514. [PMID: 26217365 PMCID: PMC4496560 DOI: 10.3389/fpls.2015.00514] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
All living organisms require iron (Fe) to carry out many crucial metabolic pathways. Despite its high concentrations in the geosphere, Fe bio-availability to plant roots can be very scarce. To cope with Fe shortage, plants can activate different strategies. For these reasons, we investigated Fe deficient Hordeum vulgare L. plants by monitoring growth, phytosiderophores (PS) release, iron content, and translocation, and DNA methylation, with respect to Fe sufficient ones. Reductions of plant growth, roots to shoots Fe translocation, and increases in PS release were found. Experiments on DNA methylation highlighted significant differences between fully and hemy-methylated sequences in Fe deficient plants, with respect to Fe sufficient plants. Eleven DNA bands differently methylated were found in starved plants. Of these, five sequences showed significant alignment to barley genes encoding for a glucosyltransferase, a putative acyl carrier protein, a peroxidase, a β-glucosidase and a transcription factor containing a Homeodomin. A resupply experiment was carried out on starved barley re-fed at 13 days after sowing (DAS), and it showed that plants did not recover after Fe addition. In fact, Fe absorption and root to shoot translocation capacities were impaired. In addition, resupplied barley showed DNA methylation/demethylation patterns very similar to that of barley grown in Fe deprivation. This last finding is very encouraging because it indicates as these variations/modifications could be transmitted to progenies.
Collapse
Affiliation(s)
- Marika Bocchini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Maria Luce Bartucca
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Simona Ciancaleoni
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Youry Pii
- Faculty of Science and Technology, Free University of BolzanoBolzano, Italy
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
- *Correspondence: Emidio Albertini, Department of Agriculture, Food and Environmental Sciences, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Daniele Del Buono
- Department of Agricultural, Food and Environmental Sciences, University of PerugiaPerugia, Italy
| |
Collapse
|
44
|
Wang H, Qi X, Chen S, Fang W, Guan Z, Teng N, Liao Y, Jiang J, Chen F. Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy. FRONTIERS IN PLANT SCIENCE 2015; 6:668. [PMID: 26379692 PMCID: PMC4550781 DOI: 10.3389/fpls.2015.00668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 08/13/2015] [Indexed: 05/06/2023]
Abstract
Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5'-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.
Collapse
Affiliation(s)
- Haibin Wang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and EquipmentNanjing, China
| | - Xiangyu Qi
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- *Correspondence: Fadi Chen and Jiafu Jiang, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China, ;
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural UniversityNanjing, China
- Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and EquipmentNanjing, China
- *Correspondence: Fadi Chen and Jiafu Jiang, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China, ;
| |
Collapse
|
45
|
Gao Y, Ran L, Kong Y, Jiang J, Sokolov V, Wang Y. Assessment of DNA methylation changes in tissue culture of Brassica napus. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414100032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Thomas M, Pingault L, Poulet A, Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV, Tatout C. Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics 2014; 15:922. [PMID: 25342325 PMCID: PMC4223845 DOI: 10.1186/1471-2164-15-922] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plant and animal methyltransferases are key enzymes involved in DNA methylation at cytosine residues, required for gene expression control and genome stability. Taking advantage of the new sequence surveys of the wheat genome recently released by the International Wheat Genome Sequencing Consortium, we identified and characterized MET1 genes in the hexaploid wheat Triticum aestivum (TaMET1). RESULTS Nine TaMET1 genes were identified and mapped on homoeologous chromosome groups 2A/2B/2D, 5A/5B/5D and 7A/7B/7D. Synteny analysis and evolution rates suggest that the genome organization of TaMET1 genes results from a whole genome duplication shared within the grass family, and a second gene duplication, which occurred specifically in the Triticeae tribe prior to the speciation of diploid wheat. Higher expression levels were observed for TaMET1 homoeologous group 2 genes compared to group 5 and 7, indicating that group 2 homoeologous genes are predominant at the transcriptional level, while group 5 evolved into pseudogenes. We show the connection between low expression levels, elevated evolution rates and unexpected enrichment in CG-dinucleotides (CG-rich isochores) at putative promoter regions of homoeologous group 5 and 7, but not of group 2 TaMET1 genes. Bisulfite sequencing reveals that these CG-rich isochores are highly methylated in a CG context, which is the expected target of TaMET1. CONCLUSIONS We retraced the evolutionary history of MET1 genes in wheat, explaining the predominance of group 2 homoeologous genes and suggest CG-DNA methylation as one of the mechanisms involved in wheat genome dynamics.
Collapse
Affiliation(s)
- Mélanie Thomas
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Lise Pingault
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Axel Poulet
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Jorge Duarte
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Mickaël Throude
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Sébastien Faure
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Jean-Philippe Pichon
- />BIOGEMMA, route d’Ennezat, Centre de Recherche de Chappes, CS 90126, 63720 Chappes, France
| | - Etienne Paux
- />UMR INRA 1095 Blaise Pascal University, Genetics Diversity & Ecophysiology of Cereals (GDEC), Clermont-Ferrand – Theix, 5 chemin de Beaulieu, 63039 Clermont-Ferrand Cedex 2, France
| | - Aline Valeska Probst
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| | - Christophe Tatout
- />UMR CNRS 6293 INSERM U 1103 Clermont Université, Genetics Reproduction and Development (GReD), 24 avenue des Landais, BP80026, 63171 Aubière Cedex, France
| |
Collapse
|
47
|
Qian Y, Xi Y, Cheng B, Zhu S. Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize. PLANT CELL REPORTS 2014; 33:1661-72. [PMID: 24950734 DOI: 10.1007/s00299-014-1645-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/05/2014] [Accepted: 06/05/2014] [Indexed: 05/10/2023]
Abstract
In this study, we identified eight DNA MTase genes in maize and the diversity of expression patterns of them was presented by EST mining, microarray and semi-quantitative expression profile analyses. DNA methylation plays a pivotal role in promoting genomic stability through diverse biological processes including regulation of gene expression during development and chromatin organization. Although this important biological process is mainly regulated by several conserved Cytosine-5 DNA methyltransferases encoded by a smaller multigene family in plants, investigation of the plant C5-MTase-encoding gene family will serve to elucidate the epigenetic mechanism diversity in plants. Recently, genome-wide identification and evolutionary analyses of the C5-MTase-encoding gene family have been characterized in multiple plant species including Arabidopsis, rice, carrot and wheat. However, little is known regarding the C5-MTase-encoding genes in the entire maize genome. Here, genome-wide identification and expression profile analyses of maize C5-MTase-encoding genes (ZmMETs) were performed from the latest version of the maize (B73) genome. Phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice) were categorized into four classes. Chromosomal location of these genes revealed that they are unevenly distributed on 6 of all 10 chromosomes with three chromosomal/segmental duplication events, suggesting that gene duplication played a key role in expansion of the maize C5-MTase-encoding gene family. Furthermore, EST expression data mining, microarray data and semi-quantitative expression profile analyses detected in the leaves by two different abiotic stress treatments have demonstrated that these genes had temporal and spatial expression pattern and exhibited different expression levels in stress treatments, suggesting that functional diversification of ZmMET genes family. Overall, our study will serve to present signification insights to explore the plant C5-MTase-encoding gene expression and function and also be beneficial for future experimental research to further unravel the mechanisms of epigenetic regulation in plants.
Collapse
Affiliation(s)
- Yexiong Qian
- Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China,
| | | | | | | |
Collapse
|
48
|
Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants. J Genet 2014; 92:629-66. [PMID: 24371187 DOI: 10.1007/s12041-013-0273-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T orC) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations.Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and transgenerational memory in plants.
Collapse
|
49
|
Cicatelli A, Todeschini V, Lingua G, Biondi S, Torrigiani P, Castiglione S. Epigenetic control of heavy metal stress response in mycorrhizal versus non-mycorrhizal poplar plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:1723-1737. [PMID: 23975714 DOI: 10.1007/s11356-013-2072-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
It was previously shown that arbuscular mycorrhizal fungi (AMF) exert a significant improvement of growth in a tolerant white poplar (Populus alba L.) clone (AL35) grown on Cu- and Zn-polluted soil via foliar alterations in the levels of defence/stress-related transcripts and molecules. However, nothing is known about the epigenetic changes which occur during tolerance acquisition in response to heavy metals (HMs) in the same mycorrhizal vs. non-mycorrhizal poplar plants. In order to analyse the epigenome in leaves of AL35 plants inoculated or not with AMF and grown in a greenhouse on multimetal polluted or unpolluted soil, the Methylation Sensitive Amplification Polymorphism (MSAP) approach was adopted to detect cytosine DNA methylation. Modest changes in cytosine methylation patterns were detected at first sampling (4 months from planting), whereas extensive alterations (hypomethylation) occurred at second sampling (after 6 months) in mycorrhizal plants grown in the presence of HMs. The sequencing of MSAP fragments led to the identification of genes belonging to several Gene Ontology categories. Seven MSAP fragments, selected on the basis of DNA methylation status in treated vs control AL35 leaves at the end of the experiment, were analysed for their transcript levels by means of qRT-PCR. Gene expression varied in treated samples relative to controls in response to HMs and/or AMF inoculation; in particular, transcripts of genes involved in RNA processing, cell wall and amino acid metabolism were upregulated in the presence of AMF with or without HMs.
Collapse
Affiliation(s)
- Angela Cicatelli
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy
| | - Valeria Todeschini
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Stefania Biondi
- Dipartimento BiGeA, Università di Bologna, 40126, Bologna, Italy
| | - Patrizia Torrigiani
- Dipartimento di Scienze Agrarie, Università di Bologna, 40127, Bologna, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia, Università di Salerno, 84084, Fisciano, SA, Italy.
| |
Collapse
|
50
|
Sahu PP, Pandey G, Sharma N, Puranik S, Muthamilarasan M, Prasad M. Epigenetic mechanisms of plant stress responses and adaptation. PLANT CELL REPORTS 2013; 32:1151-9. [PMID: 23719757 DOI: 10.1007/s00299-013-1462-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 05/20/2023]
Abstract
Epigenetics has become one of the hottest topics of research in plant functional genomics since it appears promising in deciphering and imparting stress-adaptive potential in crops and other plant species. Recently, numerous studies have provided new insights into the epigenetic control of stress adaptation. Epigenetic control of stress-induced phenotypic response of plants involves gene regulation. Growing evidence suggest that methylation of DNA in response to stress leads to the variation in phenotype. Transposon mobility, siRNA-mediated methylation and host methyltransferase activation have been implicated in this process. This review presents the current status of epigenetics of plant stress responses with a view to use this knowledge towards engineering plants for stress tolerance.
Collapse
Affiliation(s)
- Pranav Pankaj Sahu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | | | | | | | | | | |
Collapse
|