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Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.

Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö - PLoS Genet. (2014)

Bottom Line: Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites.We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele.This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Edinburgh, United Kingdom.

ABSTRACT
As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

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Related in: MedlinePlus

Comparison of CHH methylation patterns inside TE-bodies, (A) between CMT2WT and CMT2STOP accessions using the data from [7], and (B) between four replicate Col-0 wild-type and cmt2 knock-outs from [24].For each accession, the curve is to illustrate the moving average methylation level in a sliding 100 bp window. On the x-axis, the two different strands of DNA are aligned in the middle, truncated at 5 kb from the edge of the TEs.
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pgen-1004842-g004: Comparison of CHH methylation patterns inside TE-bodies, (A) between CMT2WT and CMT2STOP accessions using the data from [7], and (B) between four replicate Col-0 wild-type and cmt2 knock-outs from [24].For each accession, the curve is to illustrate the moving average methylation level in a sliding 100 bp window. On the x-axis, the two different strands of DNA are aligned in the middle, truncated at 5 kb from the edge of the TEs.

Mentions: CMT2 is a plant DNA methyltransferase that methylates mainly cytosines in CHH (H = any base but G) contexts, predominantly at transposable elements (TEs) [24], [25]. We tested the effect of CMT2STOP on genome-wide DNA methylation using 135 CMT2WT and 16 CMT2STOP accessions, for which high-quality MethylC-sequencing data was publicly available [7]. In earlier studies [24], [25], it has been shown that CMT2-mediated CHH methylation primarily affects TE-body methylation. In cmt2 knockouts in a Col-0 genetic background, this results in a near lack of CHH methylation at such sites. Here, we compared the levels of CHH-methylation across TEs between CMT2STOP and CMT2WT accessions. Our analyses revealed that the accessions carrying the CMT2STOP allele on average had a small (1%) average decrease in CHH-methylation across the TE-body compared to the CMT2WT accessions. A more detailed analysis showed that this difference was primarily due to two of 16 CMT2STOP accessions, Kz-9 and Neo-6, showing a TE-body CHH methylation pattern resembling that of the cmt2 knockouts in the data of [24]. Interestingly, none of the 135 CMT2WT accessions displayed such a decrease in TE-body CHH methylation, and hence there is a significant increase in the frequency of the cmt2 knockout TE-body CHH methylation pattern among the natural CMT2STOP accessions (P = 0.01; Fisher's exact test). Our analyses show that the methylation-pattern is more heterogeneous among the natural accessions than within the Col-0 accession, both for the CMT2STOP and CMT2WT accessions (both P = 0.01; Brown-Forsythe heterogeneity of variance test; Fig. 4). There is thus a significant association between the CMT2STOP polymorphism and decreased genome-wide TE-body CHH-methylation levels, and we show that this is apparently due to an increased frequency of the cmt2-mutant methylation phenotype. Further, the results also show a variable contribution of CMT2-independent CHH methylation pathways in the natural accessions. The reason why not all CMT2STOP accessions behave like alleles is unclear, but the variability amongst in the level of CHH-methylation across the natural accessions suggest that it is possible that CMT2-independent pathways, such as the RNA-dependent DNA-methylation pathway, compensate for the lack of CMT2 due to segregating polymorphisms also at these loci. Alternatively, CMT2STOP alleles may not be , maybe due to stop codon read-through, which is more common than previously thought [26]. Although our analyses of genome-wide methylation data have established that CMT2STOP allele has a quantitative effect on CHH methylation, further studies are needed to fully explore the link between the CMT2STOP allele, other pathways affecting genome-wide DNA-methylation and their joint contributions to the inferred association to temperature seasonality.


Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality.

Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö - PLoS Genet. (2014)

Comparison of CHH methylation patterns inside TE-bodies, (A) between CMT2WT and CMT2STOP accessions using the data from [7], and (B) between four replicate Col-0 wild-type and cmt2 knock-outs from [24].For each accession, the curve is to illustrate the moving average methylation level in a sliding 100 bp window. On the x-axis, the two different strands of DNA are aligned in the middle, truncated at 5 kb from the edge of the TEs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263395&req=5

pgen-1004842-g004: Comparison of CHH methylation patterns inside TE-bodies, (A) between CMT2WT and CMT2STOP accessions using the data from [7], and (B) between four replicate Col-0 wild-type and cmt2 knock-outs from [24].For each accession, the curve is to illustrate the moving average methylation level in a sliding 100 bp window. On the x-axis, the two different strands of DNA are aligned in the middle, truncated at 5 kb from the edge of the TEs.
Mentions: CMT2 is a plant DNA methyltransferase that methylates mainly cytosines in CHH (H = any base but G) contexts, predominantly at transposable elements (TEs) [24], [25]. We tested the effect of CMT2STOP on genome-wide DNA methylation using 135 CMT2WT and 16 CMT2STOP accessions, for which high-quality MethylC-sequencing data was publicly available [7]. In earlier studies [24], [25], it has been shown that CMT2-mediated CHH methylation primarily affects TE-body methylation. In cmt2 knockouts in a Col-0 genetic background, this results in a near lack of CHH methylation at such sites. Here, we compared the levels of CHH-methylation across TEs between CMT2STOP and CMT2WT accessions. Our analyses revealed that the accessions carrying the CMT2STOP allele on average had a small (1%) average decrease in CHH-methylation across the TE-body compared to the CMT2WT accessions. A more detailed analysis showed that this difference was primarily due to two of 16 CMT2STOP accessions, Kz-9 and Neo-6, showing a TE-body CHH methylation pattern resembling that of the cmt2 knockouts in the data of [24]. Interestingly, none of the 135 CMT2WT accessions displayed such a decrease in TE-body CHH methylation, and hence there is a significant increase in the frequency of the cmt2 knockout TE-body CHH methylation pattern among the natural CMT2STOP accessions (P = 0.01; Fisher's exact test). Our analyses show that the methylation-pattern is more heterogeneous among the natural accessions than within the Col-0 accession, both for the CMT2STOP and CMT2WT accessions (both P = 0.01; Brown-Forsythe heterogeneity of variance test; Fig. 4). There is thus a significant association between the CMT2STOP polymorphism and decreased genome-wide TE-body CHH-methylation levels, and we show that this is apparently due to an increased frequency of the cmt2-mutant methylation phenotype. Further, the results also show a variable contribution of CMT2-independent CHH methylation pathways in the natural accessions. The reason why not all CMT2STOP accessions behave like alleles is unclear, but the variability amongst in the level of CHH-methylation across the natural accessions suggest that it is possible that CMT2-independent pathways, such as the RNA-dependent DNA-methylation pathway, compensate for the lack of CMT2 due to segregating polymorphisms also at these loci. Alternatively, CMT2STOP alleles may not be , maybe due to stop codon read-through, which is more common than previously thought [26]. Although our analyses of genome-wide methylation data have established that CMT2STOP allele has a quantitative effect on CHH methylation, further studies are needed to fully explore the link between the CMT2STOP allele, other pathways affecting genome-wide DNA-methylation and their joint contributions to the inferred association to temperature seasonality.

Bottom Line: Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites.We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele.This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods.

View Article: PubMed Central - PubMed

Affiliation: Swedish University of Agricultural Sciences, Department of Clinical Sciences, Division of Computational Genetics, Uppsala, Sweden; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden; University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, Edinburgh, United Kingdom.

ABSTRACT
As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress.

Show MeSH
Related in: MedlinePlus