Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We inves...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2014-07-01
|
| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/03198 |
| _version_ | 1811253185593999360 |
|---|---|
| author | Daniela Pignatta Robert M Erdmann Elias Scheer Colette L Picard George W Bell Mary Gehring |
| author_facet | Daniela Pignatta Robert M Erdmann Elias Scheer Colette L Picard George W Bell Mary Gehring |
| author_sort | Daniela Pignatta |
| collection | DOAJ |
| description | Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. 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. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. |
| first_indexed | 2024-04-12T16:47:09Z |
| format | Article |
| id | doaj.art-7e1aa737a04d4967be19d2e4f995f303 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:47:09Z |
| publishDate | 2014-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-7e1aa737a04d4967be19d2e4f995f3032022-12-22T03:24:32ZengeLife Sciences Publications LtdeLife2050-084X2014-07-01310.7554/eLife.03198Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprintingDaniela Pignatta0Robert M Erdmann1Elias Scheer2Colette L Picard3George W Bell4Mary Gehring5Whitehead Institute for Biomedical Research, Cambridge, United StatesWhitehead Institute for Biomedical Research, Cambridge, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, United StatesWhitehead Institute for Biomedical Research, Cambridge, United StatesWhitehead Institute for Biomedical Research, Cambridge, United States; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, United StatesWhitehead Institute for Biomedical Research, Cambridge, United StatesWhitehead Institute for Biomedical Research, Cambridge, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, United StatesImprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. 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. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.https://elifesciences.org/articles/03198genomic imprintingDNA methylationnatural variationepiallelestransposable elementseed |
| spellingShingle | Daniela Pignatta Robert M Erdmann Elias Scheer Colette L Picard George W Bell Mary Gehring Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting eLife genomic imprinting DNA methylation natural variation epialleles transposable element seed |
| title | Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting |
| title_full | Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting |
| title_fullStr | Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting |
| title_full_unstemmed | Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting |
| title_short | Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting |
| title_sort | natural epigenetic polymorphisms lead to intraspecific variation in arabidopsis gene imprinting |
| topic | genomic imprinting DNA methylation natural variation epialleles transposable element seed |
| url | https://elifesciences.org/articles/03198 |
| work_keys_str_mv | AT danielapignatta naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting AT robertmerdmann naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting AT eliasscheer naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting AT colettelpicard naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting AT georgewbell naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting AT marygehring naturalepigeneticpolymorphismsleadtointraspecificvariationinarabidopsisgeneimprinting |