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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.

Pignatta D, Erdmann RM, Scheer E, Picard CL, Bell GW, Gehring M - Elife (2014)

Bottom Line: Imprinting variability could contribute to observed parent-of-origin effects on seed development.We successfully predicted imprinting in additional strains based on methylation variability.We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation.

View Article: PubMed Central - PubMed

Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.

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Genetic difference between strains can underlie differential methylation.Differences in methylation between strains can be due to genetic differences (e.g., absence of a sequence in one strain). To uncover possible genetic differences between Col and Cvi strains, we compared the set of Col-Cvi methylation difference positive windows to regions of the Cvi genome not covered by any reads in the 1001 Genomes resequencing project (http://signal.salk.edu/atg1001/index.php). We validated DMRs at one MEG (AT5G17165) and one PEG (AT1G57820) that were polymorphic between the two strains using PCR and sequencing. (A) In Cvi, the TE at the 3′ end of AT5G17165 lacks 600 nt, corresponding to a methylated region in Col and Ler. Red track, CG; blue track, CHG; green track, CHH. (B) In Cvi, the 86 nt long TE at the 5′ end of AT1G57820 has 9 SNPs, and the upstream and downstream intergenic DNA sequences have insertions and deletions compared to Col.DOI:http://dx.doi.org/10.7554/eLife.03198.022
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fig6s3: Genetic difference between strains can underlie differential methylation.Differences in methylation between strains can be due to genetic differences (e.g., absence of a sequence in one strain). To uncover possible genetic differences between Col and Cvi strains, we compared the set of Col-Cvi methylation difference positive windows to regions of the Cvi genome not covered by any reads in the 1001 Genomes resequencing project (http://signal.salk.edu/atg1001/index.php). We validated DMRs at one MEG (AT5G17165) and one PEG (AT1G57820) that were polymorphic between the two strains using PCR and sequencing. (A) In Cvi, the TE at the 3′ end of AT5G17165 lacks 600 nt, corresponding to a methylated region in Col and Ler. Red track, CG; blue track, CHG; green track, CHH. (B) In Cvi, the 86 nt long TE at the 5′ end of AT1G57820 has 9 SNPs, and the upstream and downstream intergenic DNA sequences have insertions and deletions compared to Col.DOI:http://dx.doi.org/10.7554/eLife.03198.022

Mentions: (A) HDG3 is a PEG except when Cvi is the paternal parent. Blue bars, % paternal allele expression; red bars, % maternal allele expression from combined mRNA-seq data; vertical line, expected percent paternal allele expression for a non-imprinted gene. (B) Methylation of HDG3 5′ flanking region in Col embryo, Ler embryo and endosperm, and Cvi embryo (additional analysis in Figure 6—figure supplement 1). Red track, CG; green track, CHH. (C) Methylation profile of maternal and paternal HDG3 alleles in Col x Cvi and Cvi x Col endosperm as determined by locus-specific bisulfite PCR. Red circles, CG; blue circles, CHG; green circle, CHH. Filled circles indicate methylation, whereas unmethylated positions are unfilled. (D) Methylation profile of HDG3 in Col, Ler, Cvi, Kz_9 and An_1 in leaves (http://neomorph.salk.edu/1001_epigenomes.html). (E) HDG3 is not imprinted in 6 DAP endosperm when another hypomethylated strain (Kz_9) is the pollen parent, but is a PEG in a cross with another methylated strain (An_1), as determined by sequencing RT-PCR products that span informative SNPs. Blue bars, % paternal allele expression; red bars, % maternal allele expression; vertical line, expected paternal allele expression for a non-imprinted gene. The number of RT-PCR clones sequenced is indicated. p value represents a binomial test of whether the observed maternal:total ratio is less than the expected 2:3 ratio. (F) Cartoon representation of results. Expression and methylation results for AT3G14205 and AT2G34890 are in Figure 6—figure supplement 2. Examples of genetic differences causing methylation differences are in Figure 6—figure supplement 3.


Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.

Pignatta D, Erdmann RM, Scheer E, Picard CL, Bell GW, Gehring M - Elife (2014)

Genetic difference between strains can underlie differential methylation.Differences in methylation between strains can be due to genetic differences (e.g., absence of a sequence in one strain). To uncover possible genetic differences between Col and Cvi strains, we compared the set of Col-Cvi methylation difference positive windows to regions of the Cvi genome not covered by any reads in the 1001 Genomes resequencing project (http://signal.salk.edu/atg1001/index.php). We validated DMRs at one MEG (AT5G17165) and one PEG (AT1G57820) that were polymorphic between the two strains using PCR and sequencing. (A) In Cvi, the TE at the 3′ end of AT5G17165 lacks 600 nt, corresponding to a methylated region in Col and Ler. Red track, CG; blue track, CHG; green track, CHH. (B) In Cvi, the 86 nt long TE at the 5′ end of AT1G57820 has 9 SNPs, and the upstream and downstream intergenic DNA sequences have insertions and deletions compared to Col.DOI:http://dx.doi.org/10.7554/eLife.03198.022
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fig6s3: Genetic difference between strains can underlie differential methylation.Differences in methylation between strains can be due to genetic differences (e.g., absence of a sequence in one strain). To uncover possible genetic differences between Col and Cvi strains, we compared the set of Col-Cvi methylation difference positive windows to regions of the Cvi genome not covered by any reads in the 1001 Genomes resequencing project (http://signal.salk.edu/atg1001/index.php). We validated DMRs at one MEG (AT5G17165) and one PEG (AT1G57820) that were polymorphic between the two strains using PCR and sequencing. (A) In Cvi, the TE at the 3′ end of AT5G17165 lacks 600 nt, corresponding to a methylated region in Col and Ler. Red track, CG; blue track, CHG; green track, CHH. (B) In Cvi, the 86 nt long TE at the 5′ end of AT1G57820 has 9 SNPs, and the upstream and downstream intergenic DNA sequences have insertions and deletions compared to Col.DOI:http://dx.doi.org/10.7554/eLife.03198.022
Mentions: (A) HDG3 is a PEG except when Cvi is the paternal parent. Blue bars, % paternal allele expression; red bars, % maternal allele expression from combined mRNA-seq data; vertical line, expected percent paternal allele expression for a non-imprinted gene. (B) Methylation of HDG3 5′ flanking region in Col embryo, Ler embryo and endosperm, and Cvi embryo (additional analysis in Figure 6—figure supplement 1). Red track, CG; green track, CHH. (C) Methylation profile of maternal and paternal HDG3 alleles in Col x Cvi and Cvi x Col endosperm as determined by locus-specific bisulfite PCR. Red circles, CG; blue circles, CHG; green circle, CHH. Filled circles indicate methylation, whereas unmethylated positions are unfilled. (D) Methylation profile of HDG3 in Col, Ler, Cvi, Kz_9 and An_1 in leaves (http://neomorph.salk.edu/1001_epigenomes.html). (E) HDG3 is not imprinted in 6 DAP endosperm when another hypomethylated strain (Kz_9) is the pollen parent, but is a PEG in a cross with another methylated strain (An_1), as determined by sequencing RT-PCR products that span informative SNPs. Blue bars, % paternal allele expression; red bars, % maternal allele expression; vertical line, expected paternal allele expression for a non-imprinted gene. The number of RT-PCR clones sequenced is indicated. p value represents a binomial test of whether the observed maternal:total ratio is less than the expected 2:3 ratio. (F) Cartoon representation of results. Expression and methylation results for AT3G14205 and AT2G34890 are in Figure 6—figure supplement 2. Examples of genetic differences causing methylation differences are in Figure 6—figure supplement 3.

Bottom Line: Imprinting variability could contribute to observed parent-of-origin effects on seed development.We successfully predicted imprinting in additional strains based on methylation variability.We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation.

View Article: PubMed Central - PubMed

Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.

Show MeSH
Related in: MedlinePlus