Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting.
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.
Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.Show MeSH
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.
Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.