Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice.
Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes. The most prominent example of phased nucleosomes is...
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2014-05-01
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doaj-9d0a510fe2d14e8d8af2499d0cd320212020-11-24T21:47:55ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042014-05-01105e100437810.1371/journal.pgen.1004378Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice.Yufeng WuWenli ZhangJiming JiangNucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors determine nucleosome positioning in regions that are not close to genes. We mapped both nucleosome positioning and DNase I hypersensitive site (DHS) datasets across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Phased nucleosomes were also found to flank DHSs in the human genome. Our results suggest the barrier model may represent a general feature of nucleosome organization in eukaryote genomes. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome.http://europepmc.org/articles/PMC4031139?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yufeng Wu Wenli Zhang Jiming Jiang |
spellingShingle |
Yufeng Wu Wenli Zhang Jiming Jiang Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genetics |
author_facet |
Yufeng Wu Wenli Zhang Jiming Jiang |
author_sort |
Yufeng Wu |
title |
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. |
title_short |
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. |
title_full |
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. |
title_fullStr |
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. |
title_full_unstemmed |
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. |
title_sort |
genome-wide nucleosome positioning is orchestrated by genomic regions associated with dnase i hypersensitivity in rice. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Genetics |
issn |
1553-7390 1553-7404 |
publishDate |
2014-05-01 |
description |
Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors determine nucleosome positioning in regions that are not close to genes. We mapped both nucleosome positioning and DNase I hypersensitive site (DHS) datasets across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Phased nucleosomes were also found to flank DHSs in the human genome. Our results suggest the barrier model may represent a general feature of nucleosome organization in eukaryote genomes. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. |
url |
http://europepmc.org/articles/PMC4031139?pdf=render |
work_keys_str_mv |
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