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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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Overlap of embryo-endosperm CG DMRs with previous studies.This study: DMRs identified from all matched comparisons, Gehring et al., 2009: Col-glxCol-gl and LerxLer DMRs, Ibarra et al., 2012: ColxLer and LerxCol DMRs combined. To identify the DMRs, this study and Ibarra et al. (2012) datasets were analyzed with the same analysis pipeline described in ‘Materials and methods’. Minimum overlap required between DMRs = 100 nt.DOI:http://dx.doi.org/10.7554/eLife.03198.029
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fig4s5: Overlap of embryo-endosperm CG DMRs with previous studies.This study: DMRs identified from all matched comparisons, Gehring et al., 2009: Col-glxCol-gl and LerxLer DMRs, Ibarra et al., 2012: ColxLer and LerxCol DMRs combined. To identify the DMRs, this study and Ibarra et al. (2012) datasets were analyzed with the same analysis pipeline described in ‘Materials and methods’. Minimum overlap required between DMRs = 100 nt.DOI:http://dx.doi.org/10.7554/eLife.03198.029

Mentions: (A) Number of features overlapping strain DMRs between Col and Ler or Col and Cvi embryos. (B) Number of features overlapping embryo-endosperm DMRs in Col x Cvi and Cvi x Col crosses. (C and D) 24 nt small RNA quantities (reads per million) corresponding to Col-Cvi strain (C) and Col x Cvi or Cvi x Col embryo-endosperm DMRs (D). (E) Overlap between Col-Cvi strain positive CG DMRs (more methylated in Col than Cvi) and the union of Col x Cvi and Cvi x Col embryo-endosperm CG DMRs (embryo more methylated than endosperm) corresponding to genes, TEs, and intergenic regions. Figure 4—figure supplement 1 show the distribution of all methylation differences; Figure 4—figure supplement 2 shows DMR analysis in Ler-Cvi crosses and other datasets; Figure 4—figure supplement 3 validates DMRs identified in this analysis; Figure 4—figure supplement 4 examines small RNAs at TEs and Figure 4—figure supplement 5 shows the overlap of embryo-endosperm CpG DMRs with previous studies. sRNA-seq library metrics are in Figure 4—source data 1.


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)

Overlap of embryo-endosperm CG DMRs with previous studies.This study: DMRs identified from all matched comparisons, Gehring et al., 2009: Col-glxCol-gl and LerxLer DMRs, Ibarra et al., 2012: ColxLer and LerxCol DMRs combined. To identify the DMRs, this study and Ibarra et al. (2012) datasets were analyzed with the same analysis pipeline described in ‘Materials and methods’. Minimum overlap required between DMRs = 100 nt.DOI:http://dx.doi.org/10.7554/eLife.03198.029
© Copyright Policy
Related In: Results  -  Collection

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

fig4s5: Overlap of embryo-endosperm CG DMRs with previous studies.This study: DMRs identified from all matched comparisons, Gehring et al., 2009: Col-glxCol-gl and LerxLer DMRs, Ibarra et al., 2012: ColxLer and LerxCol DMRs combined. To identify the DMRs, this study and Ibarra et al. (2012) datasets were analyzed with the same analysis pipeline described in ‘Materials and methods’. Minimum overlap required between DMRs = 100 nt.DOI:http://dx.doi.org/10.7554/eLife.03198.029
Mentions: (A) Number of features overlapping strain DMRs between Col and Ler or Col and Cvi embryos. (B) Number of features overlapping embryo-endosperm DMRs in Col x Cvi and Cvi x Col crosses. (C and D) 24 nt small RNA quantities (reads per million) corresponding to Col-Cvi strain (C) and Col x Cvi or Cvi x Col embryo-endosperm DMRs (D). (E) Overlap between Col-Cvi strain positive CG DMRs (more methylated in Col than Cvi) and the union of Col x Cvi and Cvi x Col embryo-endosperm CG DMRs (embryo more methylated than endosperm) corresponding to genes, TEs, and intergenic regions. Figure 4—figure supplement 1 show the distribution of all methylation differences; Figure 4—figure supplement 2 shows DMR analysis in Ler-Cvi crosses and other datasets; Figure 4—figure supplement 3 validates DMRs identified in this analysis; Figure 4—figure supplement 4 examines small RNAs at TEs and Figure 4—figure supplement 5 shows the overlap of embryo-endosperm CpG DMRs with previous studies. sRNA-seq library metrics are in Figure 4—source data 1.

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