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Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean
Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyle...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066788/ https://www.ncbi.nlm.nih.gov/pubmed/24799438 http://dx.doi.org/10.1093/nar/gku375 |
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author | Xu, Wei Dai, Mengyuan Li, Fei Liu, Aizhong |
author_facet | Xu, Wei Dai, Mengyuan Li, Fei Liu, Aizhong |
author_sort | Xu, Wei |
collection | PubMed |
description | Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting. |
format | Online Article Text |
id | pubmed-4066788 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40667882014-06-24 Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean Xu, Wei Dai, Mengyuan Li, Fei Liu, Aizhong Nucleic Acids Res Gene regulation, Chromatin and Epigenetics Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting. Oxford University Press 2014-07-01 2014-05-05 /pmc/articles/PMC4066788/ /pubmed/24799438 http://dx.doi.org/10.1093/nar/gku375 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene regulation, Chromatin and Epigenetics Xu, Wei Dai, Mengyuan Li, Fei Liu, Aizhong Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title | Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title_full | Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title_fullStr | Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title_full_unstemmed | Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title_short | Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
title_sort | genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066788/ https://www.ncbi.nlm.nih.gov/pubmed/24799438 http://dx.doi.org/10.1093/nar/gku375 |
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