Genomic distribution of H3K9me2 and DNA methylation in a maize genome.

DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylatio...

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Autores principales:	Patrick T West, Qing Li, Lexiang Ji, Steven R Eichten, Jawon Song, Matthew W Vaughn, Robert J Schmitz, Nathan M Springer
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fee630b24ba74a4fa3ff9e58fc150775
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spelling	oai:doaj.org-article:fee630b24ba74a4fa3ff9e58fc1507752021-11-25T06:04:41ZGenomic distribution of H3K9me2 and DNA methylation in a maize genome.1932-620310.1371/journal.pone.0105267https://doaj.org/article/fee630b24ba74a4fa3ff9e58fc1507752014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25122127/?tool=EBIhttps://doaj.org/toc/1932-6203DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.Patrick T WestQing LiLexiang JiSteven R EichtenJawon SongMatthew W VaughnRobert J SchmitzNathan M SpringerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e105267 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Patrick T West Qing Li Lexiang Ji Steven R Eichten Jawon Song Matthew W Vaughn Robert J Schmitz Nathan M Springer Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
description	DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons.
format	article
author	Patrick T West Qing Li Lexiang Ji Steven R Eichten Jawon Song Matthew W Vaughn Robert J Schmitz Nathan M Springer
author_facet	Patrick T West Qing Li Lexiang Ji Steven R Eichten Jawon Song Matthew W Vaughn Robert J Schmitz Nathan M Springer
author_sort	Patrick T West
title	Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
title_short	Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
title_full	Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
title_fullStr	Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
title_full_unstemmed	Genomic distribution of H3K9me2 and DNA methylation in a maize genome.
title_sort	genomic distribution of h3k9me2 and dna methylation in a maize genome.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/fee630b24ba74a4fa3ff9e58fc150775
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Genomic distribution of H3K9me2 and DNA methylation in a maize genome.

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