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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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Fraction of maternal small RNAs near the 5’ end of imprinted genes.Boxplots illustrating the fraction of classified 24 nt sRNA reads identified as derived from the maternally inherited genome for the set of all genes that were analyzed for imprinting, the union of all identified MEGs, and the union of all identified PEGs (Figure 1B). Windows had to exceed a threshold of five classified reads (i.e., reads that could be assigned to the maternal or paternal genome based on SNPs) to be included in the analysis. p-values were calculated using the Wilcoxon-Mann-Whitney test. *p<0.05; **p<0.01; ***p<0.001.DOI:http://dx.doi.org/10.7554/eLife.03198.033
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fig5s3: Fraction of maternal small RNAs near the 5’ end of imprinted genes.Boxplots illustrating the fraction of classified 24 nt sRNA reads identified as derived from the maternally inherited genome for the set of all genes that were analyzed for imprinting, the union of all identified MEGs, and the union of all identified PEGs (Figure 1B). Windows had to exceed a threshold of five classified reads (i.e., reads that could be assigned to the maternal or paternal genome based on SNPs) to be included in the analysis. p-values were calculated using the Wilcoxon-Mann-Whitney test. *p<0.05; **p<0.01; ***p<0.001.DOI:http://dx.doi.org/10.7554/eLife.03198.033

Mentions: (A) Average CG methylation in embryo and endosperm for the union set of PEGs, MEGs and all genes. (B) Percentage of genes with TE at indicated position. (C) Distribution of TEs and 24 nt small RNAs around endosperm imprinted MEGs (n = 85) and PEGs (n = 29) identified in at least two of three sets of reciprocal crosses. TE heatmap indicates the presence or absence of TEs according to TAIR10 annotation. 24 nt small RNA data is from ColxCvi whole seeds. Other libraries showed the same overall small RNA profile. Values were calculated in 200 nt windows extending 2 kb upstream and downstream from the 5′ and 3′ ends of the gene and 1 kb into the gene body. White indicates the absence of data. Figure 5—figure supplement 1 shows H3K27me3 profiles around imprinted genes in vegetative tissues. Figure 5—figure supplement 2 and Figure 5—figure supplement 3 further explore the distribution and allelic contribution of small RNAs associated with imprinted genes.


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)

Fraction of maternal small RNAs near the 5’ end of imprinted genes.Boxplots illustrating the fraction of classified 24 nt sRNA reads identified as derived from the maternally inherited genome for the set of all genes that were analyzed for imprinting, the union of all identified MEGs, and the union of all identified PEGs (Figure 1B). Windows had to exceed a threshold of five classified reads (i.e., reads that could be assigned to the maternal or paternal genome based on SNPs) to be included in the analysis. p-values were calculated using the Wilcoxon-Mann-Whitney test. *p<0.05; **p<0.01; ***p<0.001.DOI:http://dx.doi.org/10.7554/eLife.03198.033
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4115658&req=5

fig5s3: Fraction of maternal small RNAs near the 5’ end of imprinted genes.Boxplots illustrating the fraction of classified 24 nt sRNA reads identified as derived from the maternally inherited genome for the set of all genes that were analyzed for imprinting, the union of all identified MEGs, and the union of all identified PEGs (Figure 1B). Windows had to exceed a threshold of five classified reads (i.e., reads that could be assigned to the maternal or paternal genome based on SNPs) to be included in the analysis. p-values were calculated using the Wilcoxon-Mann-Whitney test. *p<0.05; **p<0.01; ***p<0.001.DOI:http://dx.doi.org/10.7554/eLife.03198.033
Mentions: (A) Average CG methylation in embryo and endosperm for the union set of PEGs, MEGs and all genes. (B) Percentage of genes with TE at indicated position. (C) Distribution of TEs and 24 nt small RNAs around endosperm imprinted MEGs (n = 85) and PEGs (n = 29) identified in at least two of three sets of reciprocal crosses. TE heatmap indicates the presence or absence of TEs according to TAIR10 annotation. 24 nt small RNA data is from ColxCvi whole seeds. Other libraries showed the same overall small RNA profile. Values were calculated in 200 nt windows extending 2 kb upstream and downstream from the 5′ and 3′ ends of the gene and 1 kb into the gene body. White indicates the absence of data. Figure 5—figure supplement 1 shows H3K27me3 profiles around imprinted genes in vegetative tissues. Figure 5—figure supplement 2 and Figure 5—figure supplement 3 further explore the distribution and allelic contribution of small RNAs associated with imprinted genes.

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