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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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Imprinted genes are expressed at multiple stages of development.(A) Expression of 199 MEGs and 82 PEGs in leaves, shoot apex (Sh), flowers, roots (R), pollen (P), and seeds at various stages of development. Tissue series data was downloaded using the e-Northern expression tool from the Bio-Analytic Resource (Toufighi et al., 2005). (B) Expression of MEGs and PEGs in whole seeds (WS), embryo proper (EP), suspensor (S), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), general seed coat (SC) and chalazal seed coat (CSC). Data is from Belmonte et al., 2013. Each tissue is organized by increasing developmental age from pre-globular to mature green. Data was clustered and visualized using GENE-E. Gene order is the same between A and B.DOI:http://dx.doi.org/10.7554/eLife.03198.012
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fig1s4: Imprinted genes are expressed at multiple stages of development.(A) Expression of 199 MEGs and 82 PEGs in leaves, shoot apex (Sh), flowers, roots (R), pollen (P), and seeds at various stages of development. Tissue series data was downloaded using the e-Northern expression tool from the Bio-Analytic Resource (Toufighi et al., 2005). (B) Expression of MEGs and PEGs in whole seeds (WS), embryo proper (EP), suspensor (S), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), general seed coat (SC) and chalazal seed coat (CSC). Data is from Belmonte et al., 2013. Each tissue is organized by increasing developmental age from pre-globular to mature green. Data was clustered and visualized using GENE-E. Gene order is the same between A and B.DOI:http://dx.doi.org/10.7554/eLife.03198.012

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.


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)

Imprinted genes are expressed at multiple stages of development.(A) Expression of 199 MEGs and 82 PEGs in leaves, shoot apex (Sh), flowers, roots (R), pollen (P), and seeds at various stages of development. Tissue series data was downloaded using the e-Northern expression tool from the Bio-Analytic Resource (Toufighi et al., 2005). (B) Expression of MEGs and PEGs in whole seeds (WS), embryo proper (EP), suspensor (S), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), general seed coat (SC) and chalazal seed coat (CSC). Data is from Belmonte et al., 2013. Each tissue is organized by increasing developmental age from pre-globular to mature green. Data was clustered and visualized using GENE-E. Gene order is the same between A and B.DOI:http://dx.doi.org/10.7554/eLife.03198.012
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getmorefigures.php?uid=PMC4115658&req=5

fig1s4: Imprinted genes are expressed at multiple stages of development.(A) Expression of 199 MEGs and 82 PEGs in leaves, shoot apex (Sh), flowers, roots (R), pollen (P), and seeds at various stages of development. Tissue series data was downloaded using the e-Northern expression tool from the Bio-Analytic Resource (Toufighi et al., 2005). (B) Expression of MEGs and PEGs in whole seeds (WS), embryo proper (EP), suspensor (S), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), general seed coat (SC) and chalazal seed coat (CSC). Data is from Belmonte et al., 2013. Each tissue is organized by increasing developmental age from pre-globular to mature green. Data was clustered and visualized using GENE-E. Gene order is the same between A and B.DOI:http://dx.doi.org/10.7554/eLife.03198.012
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.

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