Oligonucleotide sequence motifs as nucleosome positioning signals.

To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach ent...

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Autores principales:	Clayton K Collings, Alfonso G Fernandez, Chad G Pitschka, Troy B Hawkins, John N Anderson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6336e6c4ee3941a1be223c2fa5f9d714
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spelling	oai:doaj.org-article:6336e6c4ee3941a1be223c2fa5f9d7142021-12-02T20:21:12ZOligonucleotide sequence motifs as nucleosome positioning signals.1932-620310.1371/journal.pone.0010933https://doaj.org/article/6336e6c4ee3941a1be223c2fa5f9d7142010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20532171/?tool=EBIhttps://doaj.org/toc/1932-6203To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3-4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of positioned nucleosomes.Clayton K CollingsAlfonso G FernandezChad G PitschkaTroy B HawkinsJohn N AndersonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 6, p e10933 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Clayton K Collings Alfonso G Fernandez Chad G Pitschka Troy B Hawkins John N Anderson Oligonucleotide sequence motifs as nucleosome positioning signals.
description	To gain a better understanding of the sequence patterns that characterize positioned nucleosomes, we first performed an analysis of the periodicities of the 256 tetranucleotides in a yeast genome-wide library of nucleosomal DNA sequences that was prepared by in vitro reconstitution. The approach entailed the identification and analysis of 24 unique tetranucleotides that were defined by 8 consensus sequences. These consensus sequences were shown to be responsible for most if not all of the tetranucleotide and dinucleotide periodicities displayed by the entire library, demonstrating that the periodicities of dinucleotides that characterize the yeast genome are, in actuality, due primarily to the 8 consensus sequences. A novel combination of experimental and bioinformatic approaches was then used to show that these tetranucleotides are important for preferred formation of nucleosomes at specific sites along DNA in vitro. These results were then compared to tetranucleotide patterns in genome-wide in vivo libraries from yeast and C. elegans in order to assess the contributions of DNA sequence in the control of nucleosome residency in the cell. These comparisons revealed striking similarities in the tetranucleotide occurrence profiles that are likely to be involved in nucleosome positioning in both in vitro and in vivo libraries, suggesting that DNA sequence is an important factor in the control of nucleosome placement in vivo. However, the strengths of the tetranucleotide periodicities were 3-4 fold higher in the in vitro as compared to the in vivo libraries, which implies that DNA sequence plays less of a role in dictating nucleosome positions in vivo. The results of this study have important implications for models of sequence-dependent positioning since they suggest that a defined subset of tetranucleotides is involved in preferred nucleosome occupancy and that these tetranucleotides are the major source of the dinucleotide periodicities that are characteristic of positioned nucleosomes.
format	article
author	Clayton K Collings Alfonso G Fernandez Chad G Pitschka Troy B Hawkins John N Anderson
author_facet	Clayton K Collings Alfonso G Fernandez Chad G Pitschka Troy B Hawkins John N Anderson
author_sort	Clayton K Collings
title	Oligonucleotide sequence motifs as nucleosome positioning signals.
title_short	Oligonucleotide sequence motifs as nucleosome positioning signals.
title_full	Oligonucleotide sequence motifs as nucleosome positioning signals.
title_fullStr	Oligonucleotide sequence motifs as nucleosome positioning signals.
title_full_unstemmed	Oligonucleotide sequence motifs as nucleosome positioning signals.
title_sort	oligonucleotide sequence motifs as nucleosome positioning signals.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/6336e6c4ee3941a1be223c2fa5f9d714
work_keys_str_mv	AT claytonkcollings oligonucleotidesequencemotifsasnucleosomepositioningsignals AT alfonsogfernandez oligonucleotidesequencemotifsasnucleosomepositioningsignals AT chadgpitschka oligonucleotidesequencemotifsasnucleosomepositioningsignals AT troybhawkins oligonucleotidesequencemotifsasnucleosomepositioningsignals AT johnnanderson oligonucleotidesequencemotifsasnucleosomepositioningsignals
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Oligonucleotide sequence motifs as nucleosome positioning signals.

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