1
|
Kumar BKP, Beaubiat S, Yadav CB, Eshed R, Arazi T, Sherman A, Bouché N. Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase. Cell Mol Life Sci 2024; 81:222. [PMID: 38767725 PMCID: PMC11106227 DOI: 10.1007/s00018-024-05255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Epigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1. PURPOSE Here, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system. RESULTS Methylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification. CONCLUSION Collectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.
Collapse
Affiliation(s)
- Bapatla Kesava Pavan Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel
- Molecular Biology, Acrannolife Genomics Private Limited, Chennai, Tamilnadu, 600035, India
| | - Sébastien Beaubiat
- INRAE, AgroParisTech, Institute Jean-Pierre Bourgin for Plant Sciences (IJPB), Université Paris-Saclay, 78000, Versailles, France
| | - Chandra Bhan Yadav
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel
- Department of Genetics, Genomics, and Breeding, NIAB-EMR, East Malling, East Malling, ME19 6BJ, UK
| | - Ravit Eshed
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel
| | - Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel.
| | - Nicolas Bouché
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Derech Hamacabim 68, Rishon Lezion, Israel.
| |
Collapse
|
2
|
Epigenetic Changes Occurring in Plant Inbreeding. Int J Mol Sci 2023; 24:ijms24065407. [PMID: 36982483 PMCID: PMC10048984 DOI: 10.3390/ijms24065407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Inbreeding is the crossing of closely related individuals in nature or a plantation or self-pollinating plants, which produces plants with high homozygosity. This process can reduce genetic diversity in the offspring and decrease heterozygosity, whereas inbred depression (ID) can often reduce viability. Inbred depression is common in plants and animals and has played a significant role in evolution. In the review, we aim to show that inbreeding can, through the action of epigenetic mechanisms, affect gene expression, resulting in changes in the metabolism and phenotype of organisms. This is particularly important in plant breeding because epigenetic profiles can be linked to the deterioration or improvement of agriculturally important characteristics.
Collapse
|
3
|
Simon M, Durand S, Ricou A, Vrielynck N, Mayjonade B, Gouzy J, Boyer R, Roux F, Camilleri C, Budar F. APOK3, a pollen killer antidote in Arabidopsis thaliana. Genetics 2022; 221:6603116. [PMID: 35666201 DOI: 10.1093/genetics/iyac089] [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: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
The principles of heredity state that the two alleles carried by a heterozygote are equally transmitted to the progeny. However, genomic regions that escape this rule have been reported in many organisms. It is notably the case of genetic loci referred to as gamete killers, where one allele enhances its transmission by causing the death of the gametes that do not carry it. Gamete killers are of great interest, particularly to understand mechanisms of evolution and speciation. Although being common in plants, only a few, all in rice, have so far been deciphered to the causal genes. Here, we studied a pollen killer found in hybrids between two accessions of Arabidopsis thaliana. Exploring natural variation, we observed this pollen killer in many crosses within the species. Genetic analyses revealed that three genetically linked elements are necessary for pollen killer activity. Using mutants, we showed that this pollen killer works according to a poison-antidote model, where the poison kills pollen grains not producing the antidote. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. De novo genomic sequencing in twelve natural variants with different behaviors regarding the pollen killer revealed a hyper variable locus, with important structural variations particularly in killer genotypes, where the antidote gene recently underwent duplications. Our results strongly suggest that the gene has newly evolved within A. thaliana. Finally, we identified in the protein sequence polymorphisms related to its antidote activity.
Collapse
Affiliation(s)
- Matthieu Simon
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Stéphanie Durand
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Anthony Ricou
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Nathalie Vrielynck
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | | | - Jérôme Gouzy
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Roxane Boyer
- INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France(doi : 10.15454/1.5572370921303193E12)
| | - Fabrice Roux
- LIPME,Université de Toulouse,INRAE,CNRS, 31326 Castanet-Tolosan, France
| | - Christine Camilleri
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Françoise Budar
- Université Paris-Saclay,INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| |
Collapse
|
4
|
Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
Collapse
Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| |
Collapse
|
5
|
The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles. Int J Mol Sci 2021; 22:ijms22168618. [PMID: 34445323 PMCID: PMC8395315 DOI: 10.3390/ijms22168618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
Collapse
|
6
|
Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, Gy I, Camilleri C, Effgen S, Koornneef M, Pecinka A, Loudet O, Schneeberger K. The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Mol Biol Evol 2021; 38:1225-1240. [PMID: 33247726 PMCID: PMC8042742 DOI: 10.1093/molbev/msaa306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.
Collapse
Affiliation(s)
- Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vipul Patel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Klasen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Petra Pecinkova
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sigi Effgen
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czech Republic
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
7
|
Bose S, Suescún AV, Song J, Castillo-González C, Aklilu BB, Branham E, Lynch R, Shippen DE. tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. PLANT CELL REPORTS 2020; 39:1669-1685. [PMID: 32959123 PMCID: PMC7655638 DOI: 10.1007/s00299-020-02594-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE: tRNA Adenosine Deaminase 3 helps to sustain telomere tracts in a telomerase-independent fashion, likely through regulating cellular metabolism. Telomere length maintenance is influenced by a complex web of chromatin and metabolism-related factors. We previously reported that a lncRNA termed AtTER2 regulates telomerase activity in Arabidopsis thaliana in response to DNA damage. AtTER2 was initially shown to partially overlap with the 5' UTR of the tRNA ADENOSINE DEAMINASE 3 (TAD3) gene. However, updated genome annotation showed that AtTER2 was completely embedded in TAD3, raising the possibility that phenotypes ascribed to AtTER2 could be derived from TAD3. Here we show through strand-specific RNA-Seq, strand-specific qRT-PCR and bioinformatic analyses that AtTER2 does not encode a stable lncRNA. Further examination of the original tad3 (ter2-1/tad3-1) mutant revealed expression of an antisense transcript driven by a cryptic promoter in the T-DNA. Hence, a new hypomorphic allele of TAD3 (tad3-2) was examined. tad3-2 mutants showed hypersensitivity to DNA damage, but no deregulation of telomerase, suggesting that the telomerase phenotype of tad3-1 mutants reflects an off-target effect. Unexpectedly, however, tad3-2 plants displayed progressive loss of telomeric DNA over successive generations that was not accompanied by alteration of terminal architecture or end protection. The phenotype was exacerbated in plants lacking the telomerase processivity factor POT1a, indicating that TAD3 promotes telomere maintenance through a non-canonical, telomerase-independent pathway. The transcriptome of tad3-2 mutants revealed significant dysregulation of genes involved in auxin signaling and glucosinolate biosynthesis, pathways that intersect the stress response, cell cycle regulation and DNA metabolism. These findings indicate that the TAD3 locus indirectly contributes to telomere length homeostasis by altering the metabolic profile in Arabidopsis.
Collapse
Affiliation(s)
- Sreyashree Bose
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ana Victoria Suescún
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Facultad de Ciencias, Instituto de Ciencias Ambientales Y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | | | - Behailu Birhanu Aklilu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- KWS Gateway Research Center, LLC, 1005 N Warson Rd, BRDG Park, St. Louis, MO, 63132, USA
| | - Erica Branham
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Ryan Lynch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Department of Biochemistry and Biophysics, 300 Olsen Blvd, Room 413, College Station, TX, 77843-2128, USA.
| |
Collapse
|
8
|
Vaid N, Ishihara H, Plötner B, Sageman-Furnas K, Wiszniewski A, Laitinen RAE. Leaf chlorosis in Arabidopsis thaliana hybrids is associated with transgenerational decline and imbalanced ribosome number. THE NEW PHYTOLOGIST 2020; 228:989-1000. [PMID: 32557724 DOI: 10.1111/nph.16752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 05/09/2023]
Abstract
The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD-box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this study, we use a sophisticated genetic approach to investigate genes underlying hybrid chlorosis. Sequence comparisons, DNA methylation inhibitor drug treatment and segregation analysis were used to investigate the epigenetic regulation of hybrid chlorosis. Relative rRNA numbers were quantified using real-time quantitative PCR. We confirmed the causality of AtRH18 and provided evidence for the involvement of the promoter region of AtRH18 in the hybrid chlorosis. Furthermore, AtMOM1 from the second parent was identified as the likely candidate gene on chromosome 1. Chlorotic hybrids displayed transgenerational decline in chlorosis, and DNA demethylation experiment restored chlorophyll levels in chlorotic hybrids. Quantification of rRNA indicated that hybrid chlorosis was associated with an imbalance in the ratio of cytosolic and plastid ribosomes. Our findings highlight that the epigenetic regulation of AtRH18 causes hybrid breakdown and provide novel information about the role of AtRH18 in plant development.
Collapse
Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Hirofumi Ishihara
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Björn Plötner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Katelyn Sageman-Furnas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Andrew Wiszniewski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| |
Collapse
|
9
|
Brock MT, Rubin MJ, DellaPenna D, Weinig C. A Nested Association Mapping Panel in Arabidopsis thaliana for Mapping and Characterizing Genetic Architecture. G3 (BETHESDA, MD.) 2020; 10:3701-3708. [PMID: 32788287 PMCID: PMC7534452 DOI: 10.1534/g3.120.401239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/08/2020] [Indexed: 12/20/2022]
Abstract
Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.
Collapse
Affiliation(s)
- Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY 82071
| | - Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY 82071
- Program in Ecology, University of Wyoming, Laramie, WY 82071
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| |
Collapse
|
10
|
Van Dooren TJM, Silveira AB, Gilbault E, Jiménez-Gómez JM, Martin A, Bach L, Tisné S, Quadrana L, Loudet O, Colot V. Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3588-3602. [PMID: 32166321 DOI: 10.1101/370320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/09/2020] [Indexed: 05/27/2023]
Abstract
There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.
Collapse
Affiliation(s)
- Tom J M Van Dooren
- CNRS - UMR 7618 Institute of Ecology and Environmental Sciences (iEES) Paris, Sorbonne University, Case 237, 4, place Jussieu, 75005 Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Antoine Martin
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| |
Collapse
|
11
|
Van Dooren TJM, Silveira AB, Gilbault E, Jiménez-Gómez JM, Martin A, Bach L, Tisné S, Quadrana L, Loudet O, Colot V. Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3588-3602. [PMID: 32166321 PMCID: PMC7307858 DOI: 10.1093/jxb/eraa132] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/09/2020] [Indexed: 05/25/2023]
Abstract
There is renewed interest in whether environmentally induced changes in phenotypes can be heritable. In plants, heritable trait variation can occur without DNA sequence mutations through epigenetic mechanisms involving DNA methylation. However, it remains unknown whether this alternative system of inheritance responds to environmental changes and if it can provide a rapid way for plants to generate adaptive heritable phenotypic variation. To assess potential transgenerational effects induced by the environment, we subjected four natural accessions of Arabidopsis thaliana together with the reference accession Col-0 to mild drought in a multi-generational experiment. As expected, plastic responses to drought were observed in each accession, as well as a number of intergenerational effects of the parental environments. However, after an intervening generation without stress, except for a very few trait-based parental effects, descendants of stressed and non-stressed plants were phenotypically indistinguishable irrespective of whether they were grown in control conditions or under water deficit. In addition, genome-wide analysis of DNA methylation and gene expression in Col-0 demonstrated that, while mild drought induced changes in the DNA methylome of exposed plants, these variants were not inherited. We conclude that mild drought stress does not induce transgenerational epigenetic effects.
Collapse
Affiliation(s)
- Tom J M Van Dooren
- CNRS - UMR 7618 Institute of Ecology and Environmental Sciences (iEES) Paris, Sorbonne University, Case 237, 4, place Jussieu, 75005 Paris, France
| | - Amanda Bortolini Silveira
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - José M Jiménez-Gómez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Antoine Martin
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Leandro Quadrana
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Vincent Colot
- Institut de Biologie de l’Ecole Normale Supérieure, (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), PSL Université Paris, Paris, France
| |
Collapse
|
12
|
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
|
13
|
Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proc Natl Acad Sci U S A 2020; 117:4874-4884. [PMID: 32071208 DOI: 10.1073/pnas.1918172117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In plants and mammals, DNA methylation plays a critical role in transcriptional silencing by delineating heterochromatin from transcriptionally active euchromatin. A homeostatic balance between heterochromatin and euchromatin is essential to genomic stability. This is evident in many diseases and mutants for heterochromatin maintenance, which are characterized by global losses of DNA methylation coupled with localized ectopic gains of DNA methylation that alter transcription. Furthermore, we have shown that genome-wide methylation patterns in Arabidopsis thaliana are highly stable over generations, with the exception of rare epialleles. However, the extent to which natural variation in the robustness of targeting DNA methylation to heterochromatin exists, and the phenotypic consequences of such variation, remain to be fully explored. Here we describe the finding that heterochromatin and genic DNA methylation are highly variable among 725 A. thaliana accessions. We found that genic DNA methylation is inversely correlated with that in heterochromatin, suggesting that certain methylation pathway(s) may be redirected to genes upon the loss of heterochromatin. This redistribution likely involves a feedback loop involving the DNA methyltransferase, CHROMOMETHYLASE 3 (CMT3), H3K9me2, and histone turnover, as highly expressed, long genes with a high density of CMT3-preferred CWG sites are more likely to be methylated. Importantly, although the presence of CG methylation in genes alone may not affect transcription, genes containing CG methylation are more likely to become methylated at non-CG sites and silenced. These findings are consistent with the hypothesis that natural variation in DNA methylation homeostasis may underlie the evolution of epialleles that alter phenotypes.
Collapse
|
14
|
Schuster-Gaul S, Geisler LJ, McGeough MD, Johnson CD, Zagorska A, Li L, Wree A, Barry V, Mikaelian I, Jih LJ, Papouchado BG, Budas G, Hoffman HM, Feldstein AE. ASK1 inhibition reduces cell death and hepatic fibrosis in an Nlrp3 mutant liver injury model. JCI Insight 2020; 5:123294. [PMID: 31996485 PMCID: PMC7098717 DOI: 10.1172/jci.insight.123294] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/18/2019] [Indexed: 12/14/2022] Open
Abstract
Hepatic inflammasome activation is considered a major contributor to liver fibrosis in NASH. Apoptosis signal-regulating kinase 1 (ASK1) is an apical mitogen-activated protein kinase that activates hepatic JNK and p38 to promote apoptosis, inflammation, and fibrosis. The aim of the current study was to investigate whether pharmacologic inhibition of ASK1 could attenuate hepatic fibrosis driven by inflammasome activation using gain-of-function NOD-like receptor protein 3 (Nlrp3) mutant mice. Tamoxifen-inducible Nlrp3 knock-in (Nlrp3A350V/+CreT-KI) mice and WT mice were administered either control chow diet or diet containing the selective ASK1 inhibitor GS-444217 for 6 weeks. Livers of Nlrp3-KI mice had increased inflammation, cell death, and fibrosis and increased phosphorylation of ASK1, p38, and c-Jun. GS-444217 reduced ASK1 pathway activation, liver cell death, and liver fibrosis. ASK1 inhibition resulted in a significant downregulation of genes involved in collagen production and extracellular matrix deposition, as well as in a reduced hepatic TNF-α expression. ASK1 inhibition also directly reduced LPS-induced gene expression of Collagen 1A1 (Col1a1) in hepatic stellate cells isolated from Nlrp3-KI mice. In conclusion, ASK1 inhibition reduced liver cell death and fibrosis downstream of inflammatory signaling induced by NLRP3. These data provide mechanistic insight into the antifibrotic mechanisms of ASK1 inhibition.
Collapse
Affiliation(s)
- Susanne Schuster-Gaul
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
- Clinic and Polyclinic for Cardiology, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Lukas Jonathan Geisler
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
- Department of Internal Medicine III, RWTH-Aachen University Hospital, Aachen, Germany
| | - Matthew D McGeough
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
| | - Casey D Johnson
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
| | | | - Li Li
- Gilead Sciences Inc., Foster City, California, USA
| | - Alexander Wree
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
- Department of Hepatology and Gastroenterology, Charité University Medical Center Berlin, Berlin, Germany
| | - Vivian Barry
- Gilead Sciences Inc., Foster City, California, USA
| | | | - Lily J Jih
- Department of Pathology, Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Bettina G Papouchado
- Department of Pathology, Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Grant Budas
- Gilead Sciences Inc., Foster City, California, USA
| | - Hal M Hoffman
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
| | - Ariel E Feldstein
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, California, USA
| |
Collapse
|
15
|
Matsubara K. How Hybrid Breakdown Can Be Handled in Rice Crossbreeding? FRONTIERS IN PLANT SCIENCE 2020; 11:575412. [PMID: 33193514 PMCID: PMC7641626 DOI: 10.3389/fpls.2020.575412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 05/16/2023]
Abstract
In crosses between genetically divergent parents, traits such as weakness and sterility often segregate in later generations. This hybrid breakdown functions as a reproductive barrier and reduces selection efficiency in crossbreeding. Here, I provide an overview of hybrid breakdown in rice crosses and discuss ways to avoid and mitigate the effects of hybrid breakdown on rice crossbreeding, including genomics-assisted breeding.
Collapse
|
16
|
Srikant T, Drost HG. How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. FRONTIERS IN PLANT SCIENCE 2020; 11:606800. [PMID: 33519857 PMCID: PMC7843580 DOI: 10.3389/fpls.2020.606800] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 05/14/2023]
Abstract
Climate adaptation through phenotypic innovation will become the main challenge for plants during global warming. Plants exhibit a plethora of mechanisms to achieve environmental and developmental plasticity by inducing dynamic alterations of gene regulation and by maximizing natural variation through large population sizes. While successful over long evolutionary time scales, most of these mechanisms lack the short-term adaptive responsiveness that global warming will require. Here, we review our current understanding of the epigenetic regulation of plant genomes, with a focus on stress-response mechanisms and transgenerational inheritance. Field and laboratory-scale experiments on plants exposed to stress have revealed a multitude of temporally controlled, mechanistic strategies integrating both genetic and epigenetic changes on the genome level. We analyze inter- and intra-species population diversity to discuss how methylome differences and transposon activation can be harnessed for short-term adaptive efforts to shape co-evolving traits in response to qualitatively new climate conditions and environmental stress.
Collapse
|
17
|
Seymour DK, Chae E, Arioz BI, Koenig D, Weigel D. Transmission ratio distortion is frequent in Arabidopsis thaliana controlled crosses. Heredity (Edinb) 2019; 122:294-304. [PMID: 29955170 PMCID: PMC6169738 DOI: 10.1038/s41437-018-0107-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/02/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. The preferential transmission of alleles or genotypes is termed transmission ratio distortion (TRD). Examples of TRD have been identified in many species, implying that they are universal, but the resolution of species-wide studies of TRD are limited. We have performed a species-wide screen for TRD in over 500 segregating F2 populations of Arabidopsis thaliana using pooled reduced-representation genome sequencing. TRD was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the biological basis of TRD in this species.
Collapse
Affiliation(s)
- Danelle K Seymour
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Burak I Arioz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Daniel Koenig
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| |
Collapse
|
18
|
Vaid N, Laitinen RAE. Diverse paths to hybrid incompatibility in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:199-213. [PMID: 30098060 DOI: 10.1111/tpj.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 05/28/2023]
Abstract
One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high-throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.
Collapse
Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| |
Collapse
|
19
|
Tao H, Song ZY, Ding XS, Yang JJ, Shi KH, Li J. Epigenetic signatures in cardiac fibrosis, special emphasis on DNA methylation and histone modification. Heart Fail Rev 2018; 23:789-799. [DOI: 10.1007/s10741-018-9694-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
20
|
Boden KA, Barber IS, Clement N, Patel T, Guetta-Baranes T, Brookes KJ, Chappell S, Craigon J, Chapman NH, Morgan K, Seymour GB, Bottley A. Methylation Profiling RIN3 and MEF2C Identifies Epigenetic Marks Associated with Sporadic Early Onset Alzheimer's Disease. J Alzheimers Dis Rep 2017; 1:97-108. [PMID: 30480232 PMCID: PMC6159661 DOI: 10.3233/adr-170015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A number of genetic loci associate with early onset Alzheimer's disease (EOAD); however, the drivers of this disease remains enigmatic. Genome wide association and in vivo modeling have shown that loss-of-function, e.g., ABCA7, reduced levels of SIRT1 and MEFF2C, or increased levels of PTK2β confer risk or link to the pathogenies. It is known that DNA methylation can profoundly affect gene expression and can impact on the composition of the proteome; therefore, the aim of this study is to assess if genes associated with sporadic EOAD (sEOAD) are differentially methylated. Epi-profiles of DNA extracted from blood and cortex were compared using a pyrosequencing platform. We identified significant group-wide hypomethylation in AD blood when compared to controls for 7 CpGs located within the 3'UTR of RIN3 (CpG1 p = 0.019, CpG2 p = 0.018, CpG3 p = 0.012, CpG4 p = 0.009, CpG5 p = 0.002, CpG6 p = 0.018, and CpG7 p = 0.013, respectively; AD/Control n = 22/26; Male/Female n = 27/21). Observed effects were not gender specific. No group wide significant differences were found in the promoter methylation of PTK2β, ABCA7, SIRT1, or MEF2C, genes known to associate with late onset AD. A rare and significant difference in methylation was observed for one CpG located upstream of the MEF2C promoter in one AD individual only (22% reduction in methylation, p = 2.0E-10; Control n = 26, AD n = 25, Male/Female n = 29/22). It is plausible aberrant methylation may mark sEOAD in blood and may manifest in some individuals as rare epi-variants for genes linked to sEOAD.
Collapse
Affiliation(s)
- Kirsty A Boden
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Imelda S Barber
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | - Naomi Clement
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tulsi Patel
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Keeley J Brookes
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | - Sally Chappell
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | - Jim Craigon
- School of Biosciences, University of Nottingham, Nottingham, UK
| | | | | | - Kevin Morgan
- Schools of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Andrew Bottley
- School of Biosciences, University of Nottingham, Nottingham, UK
| |
Collapse
|