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) Proportion of maternal (m) and paternal (p) reads for all three sets of reciprocal crosses in the endosperm. One replicate of each reciprocal cross is shown. Biases represented by each quadrant are depicted for Col-Ler endosperm crosses but apply to all graphs. Orange and pink dots represent MEGs (pink dots are MEGs in all three sets of reciprocal crosses), blue and green dots represent PEGs (blue dots are PEGs in all three sets of reciprocal crosses). Crosshairs indicate the expected log ratio for genes that lack biased expression. (B) Overlap of MEGs and PEGs in the endosperm among three sets of reciprocal crosses. Pink and blue circles: Col-Ler; brown and purple circles: Col-Cvi; yellow and gray circles: Ler-Cvi. (C) Proportion of maternal (m) and paternal (p) reads for Col-Cvi and Cvi-Ler reciprocal crosses in the embryo. Colored dots as in part A. Figure 1—figure supplement 1 shows seeds used in the experiment. Figure 1—figure supplement 2 shows validation of an imprinted gene. Figure 1—figure supplement 3 examines maternal:paternal ratios of imprinted genes identified in one set of crosses in the other two sets of reciprocal crosses. Figure 1—figure supplement 4 examines overall expression levels of imprinted genes at other stages of development. Information on mRNA-seq library metrics is in Figure 1—source data 1 and allele-specific expression information for all genes in endosperm and embryo is in Figure 1—source data 2 and Figure 1—source data 3, respectively. Figure 1—source data 4 shows the overlap among imprinted genes identified in this study and those identified in previous efforts and Figure 1—source data 5 includes independent validation of imprinted genes.
Affiliation: Whitehead Institute for Biomedical Research, Cambridge, United States.