- Email: [email protected]
The impact of climate change on plant epigenomes
Spotlight
The impact of climate change on plant epigenomes Qiong A. Liu Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
Climate change is inevitable within this century Elevated CO2 levels in the atmosphere have enhanced the greenhouse effect and resulted in climate change. The atmospheric CO2 concentration was stable at approximately 280 parts per million (ppm) for a few million years until the industrial revolution, at which point it started to rise rapidly, and is currently near 400 ppm. The Intergovernmental Panel on Climate Change (IPCC 2007; http://www.ipcc.ch/) predicted that atmospheric CO2 will reach to 550–700 ppm by 2050 and 650–1200 ppm by 2100, which means a global climatic warming of 2.5 8C or more by 2050 and of up to 6.4 8C by the end of this century. Warmer global temperatures can alter multiple climate variables, among which evaporation is expected to increase over both land and water, leading to dehydration of soils and vegetation and even more severe and longer-lasting droughts. The opposing effects of CO2 and temperature on plant growth and other traits CO2 is a major component in the photosynthetic reaction that converts solar energy into energy stored in carbohydrates and, in theory, higher CO2 levels will increase plant yield; however, temperature limits this effect because rising temperatures increase the ratio of photorespiratory loss of carbon to photosynthetic gain, therefore reducing biomass [1]. The impact of CO2 on plants and ecosystems has been assessed over multiple seasons by the free-air carbon dioxide enrichment (FACE) experiment, which imitates changes in atmospheric CO2 concentration under completely openair conditions. The overall effects on plant growth and yield were estimated to be positive, because elevated CO2 concentrations increased photosynthetic carbon gain and net primary production, improved the efficiency of nitrogen usage, and increased tolerance to drought conditions [2]. By contrast, unusually high seasonal temperatures significantly lowered biomass and grain production in a variety of crops and fruits [3], which poses a serious threat when combined with the expected need to at least double food production by 2050 to meet the demands of an increasing human population and growing reliance on biofuels (IPCC report, 2007). Experiments using Arabidopsis recapitulated the opposite effects of these two conditions on plant growth and, in addition, showed that a variety of developmental processes, such as flowering time, stomata conductance, and auxin signaling, are also affected by these conditions [4]. Therefore, it is important to better understand how plant phenotypes respond to climate change to find solutions for maintaining high yield, particularly of economically important crops. Corresponding author: Liu, Q.A. ([email protected])
The rapid adaptation of plants to climate change through epigenomic plasticity Given the accelerated timescale of climate change, plants will need to adapt to these changes rapidly. One avenue for rapid adaptation may be through modification of DNA and histone proteins, as well as through expression of noncoding small RNAs (sRNA). Collectively, the arrangement and distribution of these modifications are referred to as the (http://www.roadmapepigenomics.org/). ‘epigenome’ Changes to the epigenome are commonly caused by underlying changes in the DNA sequence and may or may not be heritable. However, in cases of a true epigenetic phenomenon, the change, which is stably inherited, cannot be correlated with a genetic change [5]. DNA methylation can alter the interactions between proteins and DNA, including transcription factors and gene regulatory regions, which affect gene expression. sRNAs, such as miRNAs and small interfering RNAs (siRNA), can silence genes by cleaving mRNAs and repressing translation. siRNAs are generated mainly in the regions of transposons and repetitive sequences. RNAdirected de novo DNA methylation (RdDM) is mediated by DNA methyltransferases in the RNA-induced silencing complex (RISC), in which siRNA binds to ARGONAUTE (AGO) protein and scans for matching transcripts by Watson–Crick base pairing. Adding or removing methyl, acetyl, ubiquitin, or phosphate groups on histone tails can alter the local chromatin state, which affects access to genetic loci. These three layers of modification are inter-related, providing cells with a dynamic and plastic mechanism for responding to developmental and environmental cues, which is particularly important for plants given their sessile nature. Moreover, these cues could give rise to novel phenotypic variation controlled by epigenetic changes that is heritable across generations. However, it is still not clear how commonly this occurs or how cells perceive and rapidly transmit environmental stress signals across generations. Recent genome-wide studies of DNA methylation in plants have begun to unveil the potential roles of epigenome reprogramming in adaptation and evolution. Using Arabidopsis plants propagated through single-seed descent for 30 generations under normal conditions, two studies uncovered spontaneously occurring epigenetic alleles that were heritable across multiple generations and could alter transcription, thus providing a mechanism for increasing phenotypic diversity without genetic mutations [6,7]. Based on single methylation polymorphisms (SMPs) at CG sites, which are commonly found within gene bodies, the epimutation rate in these plants was estimated to be 6.37 104 times faster than the spontaneous mutation rate of base substitutions [6]. These results indicate that CG sites have the potential to change rapidly their methylation status compared with genetic mutations and that this rate of change could be 503
Spotlight
Trends in Genetics September 2013, Vol. 29, No. 9
influenced by the environment. Additional evidence supporting the idea that multigenerational inheritance of epigenetic alleles occurs readily in plants comes from DNA methylation reprogramming studies in germlines. It was demonstrated that methylation in the CG and CHG contexts were largely maintained in the Arabidopsis male germline, whereas reprogramming of DNA methylation, mediated by siRNA, only occurred to a limited extent and
mainly in the CHH context in pollen [8]. The central cell, the companion cell of the egg, also undergoes DNA methylation reprogramming through RdDM, with the targeting preferences limited to euchromatic transposable elements [9]. This is in contrast to the situation in animals, where genomic DNA methylation is much erased and then reestablished in the germline each generation. Indeed, several recent studies in plants on specific loci demonstrated
Table 1. Examples of the epigenomic findings determined using the next generation sequencing approaches in Arabidopsis thaliana (Columbia-0) Sequencing types SmRNA-seq and RNA-seq
Genotype Wild type
Sample type Leaf tissues
Treatments CO2 concentrations: 430 ppm and 810 ppm; Temperatures: 22 8C and 28 8C
Genomic-seq, MethylC-seq, and RNA-seq
Strains isolated from the Northern Hemisphere with distinct genotypes, wild accessions
Leaf and mixed-stage inflorescence tissues
Natural conditions
MethylC-seq and RNA-seq
Wild type
Leaf tissues from plants of mutation-accumulation (M-A) lines grown by single-seed descent for 30 generations
Long day conditions
MethylC-seq
Wild type
Rosettes of individual 21day old plants of mutationaccumulation (M-A) lines grown by single-seed descend for 30 generations
Long-day conditions
MethylC-seq and SmRNA-seq
Transgenic plants expressing fluorescent proteins
MethylC-seq and RNA-seq
Wild type Ler and Col-0, dem-2 and fie-1 mutants, and Col-0 and Ler ecotype heterozygotes
Sperm cells and vegetative nucleus from open flowers; microspores from young flower buds Endosperm, vegetative cells, sperm nuclei, and embryos
MethylC-seq
Wild type; mutants of methyltransferases Wild type, mutants of methyltransferases and glycosylases
Five–week–old grown plants Immature (unopened) flower buds
23 8C under long day condition
MethylC-seq and RNA-seq
86 Arabidopsis genesilencing mutants; some of them are not in Col-0 background
Three-week-old leaves
Continuous light
CHIP-seq
Wild type
Seedlings, roots, and aerial parts
Liquid MS or on MS agar plates; long day conditions
MethylC-seq, SmRNA-seq, and RNA-seq
504
Continuous light
Summary of the major findings Four functional classes of differentially expressed miRNAs and their target mRNAs were identified to be regulated by elevated CO2 concentration and temperature in affecting flowering time, auxin signaling, stress responses, and carbohydrate biosynthesis DMRs targeted by RdDM are linked to SNPs, whereas SMPs and CGDMRs are truly epigenetic. Loci targeted by RdDM are epigenetically activated in pollen and seeds Transgenerational epigenetic variation in DNA methylation generates new epialleles that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation Spontaneously occurring variation rate, biased distribution, and stability of epialleles are determined; the potential contribution of sequenceindependent epialleles to plant evolution is suggested Genome reprogramming in pollen, guided by sRNA, contributes to epigenetic inheritance, transposon silencing, and imprinting Demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposons across generations Arabidopsis reference genome of DNA methylation established Arabidopsis reference genome of DNA methylation and genomewide correlations between siRNAs and DNA methylation established Interactions between different pathways and additional regulators of DNA methylation identified; DNA methylation is site-specifically regulated by different factors Four chromatin states defined by 12 histone marks with a very limited number of combinations identified, preferentially indexing active genes, repressed genes, silent repeat elements, and intergenic regions
Refs [4]
[5]
[6]
[7]
[8]
[9]
[11] [12]
[13]
[14]
Spotlight that stress-induced epigenetic changes could be potentially inherited across generations and contributed to the changes in gene expression and plant phenotypes, although it is not known for how many generations these changes are stably inherited and maintained [10]. A recent study assessed the interplay between epigenetic variation and genetic variation in a population of genotypically distinct Arabidopsis plants comprising wild accessions collected from throughout the Northern Hemisphere [5]. It was found that differentially methylated regions (DMRs) targeted by RdDM were likely linked to single nucleotide polymorphisms (SNPs), although not all of them could be explained by genotype alone [5]. However, SMPs and DMRs in the CG context appeared to be unlinked to the genome, indicating that they may be genuine epigenetic alleles [5]. Therefore, it is possible that the environment is a contributing factor that influences the epimutation rate associated with these different types of methylation variant. Thus, understanding how plant epigenomes respond to climate change and if such changes are heritable will enable better predictions about how climate change will affect plants. Why use Arabidopsis to study climate change? Improved sequencing technologies and data analysis methods provide an opportunity for profiling stress-induced changes in genomic DNA methylation (MethylC-seq), histone modifications (ChIP-seq), noncoding sRNA expression (SmRNA-seq), and transcriptomes (RNA-seq) within a short period of time and at an affordable cost. The power of these sequencing assays, collectively referred to here as epigenomic sequencing, has already been demonstrated in Arabidopsis in several aspects (Table 1). Arabidopsis is an excellent system for this type of study for several reasons. It is easy to cultivate in small spaces, such as growth chambers, with strictly controlled conditions, and is sensitive to environmental changes; thus, phenotypic changes can be readily identified. It has a rapid life cycle, enabling multiple generations to be grown within a short period of time. Compared with crops and trees, it has a relatively simple genome that can be sequenced with current technologies at a reasonable depth of coverage within hours. Finally, there is a wealth of information about its development and adaptation to environments, making functional analyses of stress-induced epigenomic changes easier. Epigenomic changes induced by climate change conditions can be assessed readily through epigenomic sequencing. The epigenetic changes that are stably inherited can be determined by sequencing several generations of plants grown under climate change conditions or reciprocal plants grown under normal conditions. RNA-seq in parallel with epigenome sequencing will help identify epialleles that affect gene expressions and plant phenotypes, and SmRNA-seq will identify RdDM. This experimental approach may reveal effects of climate change on methylomes, methylation enzymes, and other proteins that regulate DNA methylation, reprogramming in the germline, and chromatin states defined by histone modifications and their interactions with other epigenetic marks. Epigenetic changes that control phenotypes might be used as markers for
Trends in Genetics September 2013, Vol. 29, No. 9
monitoring climate change and subjected to genetic engineering to improve the plant traits permanently. Perspectives The recent findings of the Arabidopsis epigenome have raised many questions. Is epimutation a widespread phenomenon in plant species and, if so, is the rate of epimutation specific for each species? It is also unclear whether climate change will simply ramp up the rate of spontaneous epimutation, rather than generating epialleles at predictable loci. Another area for future research is the potential impact of other greenhouse gases, such as methane, ozone, and nitrous oxide, on plant epigenomes. Answers to these questions will have important ramifications for plant breeders and, ultimately, our ability to improve food security in the face of climate change. Finally, elevated CO2 is a new type of stress that plants have not been exposed to for the past several million years. Thus, in contrast to stresses such as heat, drought, salt, and pathogens, plants likely have not evolved a specific mechanism for responding to elevated CO2, and it may lead to a nonspecific, dramatic response as the plants try to find a way to deal with this significant stress. Studying the impacts of climate change in controlled experiments using Arabidopsis as a model may shed light on these questions, providing a starting ground for exploring how economically important crops will respond to the coming challenges. References 1 Long, S.P. (1991) Modification of the response of photosynthetic productivity to rising temperature by atmospheric CO2 concentrations: has its importance been underestimated? Plant Cell Environ. 14, 729–739 2 Leakey, A.D. et al. (2009) Elevated CO2 effects on plant carbon, nitrogen, and water relations: six important lessons from FACE. J. Exp. Bot. 60, 2859–2876 3 Battisti, D.S. and Naylor, R.L. (2009) Historical warnings of future food insecurity with unprecedented seasonal heat. Science 323, 240–244 4 May, P. et al. (2013) The effects of carbon dioxide and temperature on microRNA expressions in Arabidopsis development. Nat. Commun. (in press) 5 Schmitz, R.J. et al. (2013) Patterns of population epigenomic diversity. Nature 495, 193–198 6 Schmitz, R.J. et al. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369–373 7 Becker, C. et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 8 Calarco, J.P. et al. (2012) Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 9 Ibarra, C.A. et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360– 1364 10 Hirsch, S. et al. (2013) Epigenetic variation, inheritance, and selection in plant populations. Cold Spring Harb. Symp. Quant. Biol. http:// dx.doi.org/10.1101/sqb.2013.77.014605 11 Cokus, S.J. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 12 Lister, R. et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 13 Stroud, H. et al. (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364 14 Roudier, F. et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928–1938 0168-9525/$ – see front matter ß 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tig.2013.06.004 Trends in Genetics, September 2013, Vol. 29, No. 9
505
The impact of climate change on plant epigenomes Qiong A. Liu Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY 11794, USA
Climate change is inevitable within this century Elevated CO2 levels in the atmosphere have enhanced the greenhouse effect and resulted in climate change. The atmospheric CO2 concentration was stable at approximately 280 parts per million (ppm) for a few million years until the industrial revolution, at which point it started to rise rapidly, and is currently near 400 ppm. The Intergovernmental Panel on Climate Change (IPCC 2007; http://www.ipcc.ch/) predicted that atmospheric CO2 will reach to 550–700 ppm by 2050 and 650–1200 ppm by 2100, which means a global climatic warming of 2.5 8C or more by 2050 and of up to 6.4 8C by the end of this century. Warmer global temperatures can alter multiple climate variables, among which evaporation is expected to increase over both land and water, leading to dehydration of soils and vegetation and even more severe and longer-lasting droughts. The opposing effects of CO2 and temperature on plant growth and other traits CO2 is a major component in the photosynthetic reaction that converts solar energy into energy stored in carbohydrates and, in theory, higher CO2 levels will increase plant yield; however, temperature limits this effect because rising temperatures increase the ratio of photorespiratory loss of carbon to photosynthetic gain, therefore reducing biomass [1]. The impact of CO2 on plants and ecosystems has been assessed over multiple seasons by the free-air carbon dioxide enrichment (FACE) experiment, which imitates changes in atmospheric CO2 concentration under completely openair conditions. The overall effects on plant growth and yield were estimated to be positive, because elevated CO2 concentrations increased photosynthetic carbon gain and net primary production, improved the efficiency of nitrogen usage, and increased tolerance to drought conditions [2]. By contrast, unusually high seasonal temperatures significantly lowered biomass and grain production in a variety of crops and fruits [3], which poses a serious threat when combined with the expected need to at least double food production by 2050 to meet the demands of an increasing human population and growing reliance on biofuels (IPCC report, 2007). Experiments using Arabidopsis recapitulated the opposite effects of these two conditions on plant growth and, in addition, showed that a variety of developmental processes, such as flowering time, stomata conductance, and auxin signaling, are also affected by these conditions [4]. Therefore, it is important to better understand how plant phenotypes respond to climate change to find solutions for maintaining high yield, particularly of economically important crops. Corresponding author: Liu, Q.A. ([email protected])
The rapid adaptation of plants to climate change through epigenomic plasticity Given the accelerated timescale of climate change, plants will need to adapt to these changes rapidly. One avenue for rapid adaptation may be through modification of DNA and histone proteins, as well as through expression of noncoding small RNAs (sRNA). Collectively, the arrangement and distribution of these modifications are referred to as the (http://www.roadmapepigenomics.org/). ‘epigenome’ Changes to the epigenome are commonly caused by underlying changes in the DNA sequence and may or may not be heritable. However, in cases of a true epigenetic phenomenon, the change, which is stably inherited, cannot be correlated with a genetic change [5]. DNA methylation can alter the interactions between proteins and DNA, including transcription factors and gene regulatory regions, which affect gene expression. sRNAs, such as miRNAs and small interfering RNAs (siRNA), can silence genes by cleaving mRNAs and repressing translation. siRNAs are generated mainly in the regions of transposons and repetitive sequences. RNAdirected de novo DNA methylation (RdDM) is mediated by DNA methyltransferases in the RNA-induced silencing complex (RISC), in which siRNA binds to ARGONAUTE (AGO) protein and scans for matching transcripts by Watson–Crick base pairing. Adding or removing methyl, acetyl, ubiquitin, or phosphate groups on histone tails can alter the local chromatin state, which affects access to genetic loci. These three layers of modification are inter-related, providing cells with a dynamic and plastic mechanism for responding to developmental and environmental cues, which is particularly important for plants given their sessile nature. Moreover, these cues could give rise to novel phenotypic variation controlled by epigenetic changes that is heritable across generations. However, it is still not clear how commonly this occurs or how cells perceive and rapidly transmit environmental stress signals across generations. Recent genome-wide studies of DNA methylation in plants have begun to unveil the potential roles of epigenome reprogramming in adaptation and evolution. Using Arabidopsis plants propagated through single-seed descent for 30 generations under normal conditions, two studies uncovered spontaneously occurring epigenetic alleles that were heritable across multiple generations and could alter transcription, thus providing a mechanism for increasing phenotypic diversity without genetic mutations [6,7]. Based on single methylation polymorphisms (SMPs) at CG sites, which are commonly found within gene bodies, the epimutation rate in these plants was estimated to be 6.37 104 times faster than the spontaneous mutation rate of base substitutions [6]. These results indicate that CG sites have the potential to change rapidly their methylation status compared with genetic mutations and that this rate of change could be 503
Spotlight
Trends in Genetics September 2013, Vol. 29, No. 9
influenced by the environment. Additional evidence supporting the idea that multigenerational inheritance of epigenetic alleles occurs readily in plants comes from DNA methylation reprogramming studies in germlines. It was demonstrated that methylation in the CG and CHG contexts were largely maintained in the Arabidopsis male germline, whereas reprogramming of DNA methylation, mediated by siRNA, only occurred to a limited extent and
mainly in the CHH context in pollen [8]. The central cell, the companion cell of the egg, also undergoes DNA methylation reprogramming through RdDM, with the targeting preferences limited to euchromatic transposable elements [9]. This is in contrast to the situation in animals, where genomic DNA methylation is much erased and then reestablished in the germline each generation. Indeed, several recent studies in plants on specific loci demonstrated
Table 1. Examples of the epigenomic findings determined using the next generation sequencing approaches in Arabidopsis thaliana (Columbia-0) Sequencing types SmRNA-seq and RNA-seq
Genotype Wild type
Sample type Leaf tissues
Treatments CO2 concentrations: 430 ppm and 810 ppm; Temperatures: 22 8C and 28 8C
Genomic-seq, MethylC-seq, and RNA-seq
Strains isolated from the Northern Hemisphere with distinct genotypes, wild accessions
Leaf and mixed-stage inflorescence tissues
Natural conditions
MethylC-seq and RNA-seq
Wild type
Leaf tissues from plants of mutation-accumulation (M-A) lines grown by single-seed descent for 30 generations
Long day conditions
MethylC-seq
Wild type
Rosettes of individual 21day old plants of mutationaccumulation (M-A) lines grown by single-seed descend for 30 generations
Long-day conditions
MethylC-seq and SmRNA-seq
Transgenic plants expressing fluorescent proteins
MethylC-seq and RNA-seq
Wild type Ler and Col-0, dem-2 and fie-1 mutants, and Col-0 and Ler ecotype heterozygotes
Sperm cells and vegetative nucleus from open flowers; microspores from young flower buds Endosperm, vegetative cells, sperm nuclei, and embryos
MethylC-seq
Wild type; mutants of methyltransferases Wild type, mutants of methyltransferases and glycosylases
Five–week–old grown plants Immature (unopened) flower buds
23 8C under long day condition
MethylC-seq and RNA-seq
86 Arabidopsis genesilencing mutants; some of them are not in Col-0 background
Three-week-old leaves
Continuous light
CHIP-seq
Wild type
Seedlings, roots, and aerial parts
Liquid MS or on MS agar plates; long day conditions
MethylC-seq, SmRNA-seq, and RNA-seq
504
Continuous light
Summary of the major findings Four functional classes of differentially expressed miRNAs and their target mRNAs were identified to be regulated by elevated CO2 concentration and temperature in affecting flowering time, auxin signaling, stress responses, and carbohydrate biosynthesis DMRs targeted by RdDM are linked to SNPs, whereas SMPs and CGDMRs are truly epigenetic. Loci targeted by RdDM are epigenetically activated in pollen and seeds Transgenerational epigenetic variation in DNA methylation generates new epialleles that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation Spontaneously occurring variation rate, biased distribution, and stability of epialleles are determined; the potential contribution of sequenceindependent epialleles to plant evolution is suggested Genome reprogramming in pollen, guided by sRNA, contributes to epigenetic inheritance, transposon silencing, and imprinting Demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposons across generations Arabidopsis reference genome of DNA methylation established Arabidopsis reference genome of DNA methylation and genomewide correlations between siRNAs and DNA methylation established Interactions between different pathways and additional regulators of DNA methylation identified; DNA methylation is site-specifically regulated by different factors Four chromatin states defined by 12 histone marks with a very limited number of combinations identified, preferentially indexing active genes, repressed genes, silent repeat elements, and intergenic regions
Refs [4]
[5]
[6]
[7]
[8]
[9]
[11] [12]
[13]
[14]
Spotlight that stress-induced epigenetic changes could be potentially inherited across generations and contributed to the changes in gene expression and plant phenotypes, although it is not known for how many generations these changes are stably inherited and maintained [10]. A recent study assessed the interplay between epigenetic variation and genetic variation in a population of genotypically distinct Arabidopsis plants comprising wild accessions collected from throughout the Northern Hemisphere [5]. It was found that differentially methylated regions (DMRs) targeted by RdDM were likely linked to single nucleotide polymorphisms (SNPs), although not all of them could be explained by genotype alone [5]. However, SMPs and DMRs in the CG context appeared to be unlinked to the genome, indicating that they may be genuine epigenetic alleles [5]. Therefore, it is possible that the environment is a contributing factor that influences the epimutation rate associated with these different types of methylation variant. Thus, understanding how plant epigenomes respond to climate change and if such changes are heritable will enable better predictions about how climate change will affect plants. Why use Arabidopsis to study climate change? Improved sequencing technologies and data analysis methods provide an opportunity for profiling stress-induced changes in genomic DNA methylation (MethylC-seq), histone modifications (ChIP-seq), noncoding sRNA expression (SmRNA-seq), and transcriptomes (RNA-seq) within a short period of time and at an affordable cost. The power of these sequencing assays, collectively referred to here as epigenomic sequencing, has already been demonstrated in Arabidopsis in several aspects (Table 1). Arabidopsis is an excellent system for this type of study for several reasons. It is easy to cultivate in small spaces, such as growth chambers, with strictly controlled conditions, and is sensitive to environmental changes; thus, phenotypic changes can be readily identified. It has a rapid life cycle, enabling multiple generations to be grown within a short period of time. Compared with crops and trees, it has a relatively simple genome that can be sequenced with current technologies at a reasonable depth of coverage within hours. Finally, there is a wealth of information about its development and adaptation to environments, making functional analyses of stress-induced epigenomic changes easier. Epigenomic changes induced by climate change conditions can be assessed readily through epigenomic sequencing. The epigenetic changes that are stably inherited can be determined by sequencing several generations of plants grown under climate change conditions or reciprocal plants grown under normal conditions. RNA-seq in parallel with epigenome sequencing will help identify epialleles that affect gene expressions and plant phenotypes, and SmRNA-seq will identify RdDM. This experimental approach may reveal effects of climate change on methylomes, methylation enzymes, and other proteins that regulate DNA methylation, reprogramming in the germline, and chromatin states defined by histone modifications and their interactions with other epigenetic marks. Epigenetic changes that control phenotypes might be used as markers for
Trends in Genetics September 2013, Vol. 29, No. 9
monitoring climate change and subjected to genetic engineering to improve the plant traits permanently. Perspectives The recent findings of the Arabidopsis epigenome have raised many questions. Is epimutation a widespread phenomenon in plant species and, if so, is the rate of epimutation specific for each species? It is also unclear whether climate change will simply ramp up the rate of spontaneous epimutation, rather than generating epialleles at predictable loci. Another area for future research is the potential impact of other greenhouse gases, such as methane, ozone, and nitrous oxide, on plant epigenomes. Answers to these questions will have important ramifications for plant breeders and, ultimately, our ability to improve food security in the face of climate change. Finally, elevated CO2 is a new type of stress that plants have not been exposed to for the past several million years. Thus, in contrast to stresses such as heat, drought, salt, and pathogens, plants likely have not evolved a specific mechanism for responding to elevated CO2, and it may lead to a nonspecific, dramatic response as the plants try to find a way to deal with this significant stress. Studying the impacts of climate change in controlled experiments using Arabidopsis as a model may shed light on these questions, providing a starting ground for exploring how economically important crops will respond to the coming challenges. References 1 Long, S.P. (1991) Modification of the response of photosynthetic productivity to rising temperature by atmospheric CO2 concentrations: has its importance been underestimated? Plant Cell Environ. 14, 729–739 2 Leakey, A.D. et al. (2009) Elevated CO2 effects on plant carbon, nitrogen, and water relations: six important lessons from FACE. J. Exp. Bot. 60, 2859–2876 3 Battisti, D.S. and Naylor, R.L. (2009) Historical warnings of future food insecurity with unprecedented seasonal heat. Science 323, 240–244 4 May, P. et al. (2013) The effects of carbon dioxide and temperature on microRNA expressions in Arabidopsis development. Nat. Commun. (in press) 5 Schmitz, R.J. et al. (2013) Patterns of population epigenomic diversity. Nature 495, 193–198 6 Schmitz, R.J. et al. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369–373 7 Becker, C. et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245–249 8 Calarco, J.P. et al. (2012) Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 9 Ibarra, C.A. et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360– 1364 10 Hirsch, S. et al. (2013) Epigenetic variation, inheritance, and selection in plant populations. Cold Spring Harb. Symp. Quant. Biol. http:// dx.doi.org/10.1101/sqb.2013.77.014605 11 Cokus, S.J. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 12 Lister, R. et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 13 Stroud, H. et al. (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364 14 Roudier, F. et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928–1938 0168-9525/$ – see front matter ß 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tig.2013.06.004 Trends in Genetics, September 2013, Vol. 29, No. 9
505