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Seed genome hypomethylated regions are enriched in transcription factor genes
The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126732/ https://www.ncbi.nlm.nih.gov/pubmed/30104383 http://dx.doi.org/10.1073/pnas.1811017115 |
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author | Chen, Min Lin, Jer-Young Hur, Jungim Pelletier, Julie M. Baden, Russell Pellegrini, Matteo Harada, John J. Goldberg, Robert B. |
author_facet | Chen, Min Lin, Jer-Young Hur, Jungim Pelletier, Julie M. Baden, Russell Pellegrini, Matteo Harada, John J. Goldberg, Robert B. |
author_sort | Chen, Min |
collection | PubMed |
description | The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from postfertilization through dormancy and germination for regions that contain <5% or <0.4% bulk methylation in CG, CHG, and CHH contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5–76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor (TF) genes and other developmental genes that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue, and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development, probably by the action of specific TFs and epigenetic events at the chromatin level. |
format | Online Article Text |
id | pubmed-6126732 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-61267322018-09-07 Seed genome hypomethylated regions are enriched in transcription factor genes Chen, Min Lin, Jer-Young Hur, Jungim Pelletier, Julie M. Baden, Russell Pellegrini, Matteo Harada, John J. Goldberg, Robert B. Proc Natl Acad Sci U S A PNAS Plus The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from postfertilization through dormancy and germination for regions that contain <5% or <0.4% bulk methylation in CG, CHG, and CHH contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5–76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor (TF) genes and other developmental genes that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue, and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development, probably by the action of specific TFs and epigenetic events at the chromatin level. National Academy of Sciences 2018-08-28 2018-08-13 /pmc/articles/PMC6126732/ /pubmed/30104383 http://dx.doi.org/10.1073/pnas.1811017115 Text en Copyright © 2018 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/ This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | PNAS Plus Chen, Min Lin, Jer-Young Hur, Jungim Pelletier, Julie M. Baden, Russell Pellegrini, Matteo Harada, John J. Goldberg, Robert B. Seed genome hypomethylated regions are enriched in transcription factor genes |
title | Seed genome hypomethylated regions are enriched in transcription factor genes |
title_full | Seed genome hypomethylated regions are enriched in transcription factor genes |
title_fullStr | Seed genome hypomethylated regions are enriched in transcription factor genes |
title_full_unstemmed | Seed genome hypomethylated regions are enriched in transcription factor genes |
title_short | Seed genome hypomethylated regions are enriched in transcription factor genes |
title_sort | seed genome hypomethylated regions are enriched in transcription factor genes |
topic | PNAS Plus |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126732/ https://www.ncbi.nlm.nih.gov/pubmed/30104383 http://dx.doi.org/10.1073/pnas.1811017115 |
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