Nucleosome positioning sequence patterns as packing or regulatory.
Nucleosome positioning DNA sequence patterns (NPS)-usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA-at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene expression. Statistically, NPS are defined as o...
| _version_ | 1826574473611968512 |
|---|---|
| author | Erinija Pranckeviciene Sergey Hosid Nathan Liang Ilya Ioshikhes |
| author_facet | Erinija Pranckeviciene Sergey Hosid Nathan Liang Ilya Ioshikhes |
| author_sort | Erinija Pranckeviciene |
| collection | DOAJ |
| description | Nucleosome positioning DNA sequence patterns (NPS)-usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA-at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene expression. Statistically, NPS are defined as oscillations of the dinucleotide periodicity of about 10 base pairs (bp) which reflects the double helix period. We compared the nucleosomal DNA patterns in mouse, human and yeast organisms and observed few distinctive patterns that can be termed as packing and regulatory referring to distinctive modes of chromatin function. For the first time the NPS patterns in nucleus accumbens cells (NAC) in mouse brain were characterized and compared to the patterns in human CD4+ and apoptotic lymphocyte cells and well studied patterns in yeast. The NPS patterns in human CD4+ cells and mouse brain cells had very high positive correlation. However, there was no correlation between them and patterns in human apoptotic lymphocyte cells and yeast, but the latter two were highly correlated with each other. By their dinucleotide arrangements the analyzed NPS patterns classified into stable canonical WW/SS (W = A or T and S = C or G dinucleotide) and less stable RR/YY (R = A or G and Y = C or T dinucleotide) patterns and anti-patterns. In the anti-patterns positioning of the dinucleotides is flipped compared to those in the regular patterns. Stable canonical WW/SS patterns and anti-patterns are ubiquitously observed in many organisms and they had high resemblance between yeast and human apoptotic cells. Less stable RR/YY patterns had higher positive correlation between mouse and normal human cells. Our analysis and evidence from scientific literature lead to idea that various distinct patterns in nucleosomal DNA can be related to the two roles of the chromatin: packing (WW/SS) and regulatory (RR/YY and "anti"). |
| first_indexed | 2024-12-20T03:06:05Z |
| format | Article |
| id | doaj.art-9a03bf4cc06c4e4ebf4794f632334119 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2025-03-14T12:59:22Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-9a03bf4cc06c4e4ebf4794f6323341192025-03-02T05:31:07ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-01-01161e100736510.1371/journal.pcbi.1007365Nucleosome positioning sequence patterns as packing or regulatory.Erinija PranckevicieneSergey HosidNathan LiangIlya IoshikhesNucleosome positioning DNA sequence patterns (NPS)-usually distributions of particular dinucleotides or other sequence elements in nucleosomal DNA-at least partially determine chromatin structure and arrangements of nucleosomes that in turn affect gene expression. Statistically, NPS are defined as oscillations of the dinucleotide periodicity of about 10 base pairs (bp) which reflects the double helix period. We compared the nucleosomal DNA patterns in mouse, human and yeast organisms and observed few distinctive patterns that can be termed as packing and regulatory referring to distinctive modes of chromatin function. For the first time the NPS patterns in nucleus accumbens cells (NAC) in mouse brain were characterized and compared to the patterns in human CD4+ and apoptotic lymphocyte cells and well studied patterns in yeast. The NPS patterns in human CD4+ cells and mouse brain cells had very high positive correlation. However, there was no correlation between them and patterns in human apoptotic lymphocyte cells and yeast, but the latter two were highly correlated with each other. By their dinucleotide arrangements the analyzed NPS patterns classified into stable canonical WW/SS (W = A or T and S = C or G dinucleotide) and less stable RR/YY (R = A or G and Y = C or T dinucleotide) patterns and anti-patterns. In the anti-patterns positioning of the dinucleotides is flipped compared to those in the regular patterns. Stable canonical WW/SS patterns and anti-patterns are ubiquitously observed in many organisms and they had high resemblance between yeast and human apoptotic cells. Less stable RR/YY patterns had higher positive correlation between mouse and normal human cells. Our analysis and evidence from scientific literature lead to idea that various distinct patterns in nucleosomal DNA can be related to the two roles of the chromatin: packing (WW/SS) and regulatory (RR/YY and "anti").https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1007365/2/pcbi.1007365.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210221%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210221T071950Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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 |
| spellingShingle | Erinija Pranckeviciene Sergey Hosid Nathan Liang Ilya Ioshikhes Nucleosome positioning sequence patterns as packing or regulatory. PLoS Computational Biology |
| title | Nucleosome positioning sequence patterns as packing or regulatory. |
| title_full | Nucleosome positioning sequence patterns as packing or regulatory. |
| title_fullStr | Nucleosome positioning sequence patterns as packing or regulatory. |
| title_full_unstemmed | Nucleosome positioning sequence patterns as packing or regulatory. |
| title_short | Nucleosome positioning sequence patterns as packing or regulatory. |
| title_sort | nucleosome positioning sequence patterns as packing or regulatory |
| url | https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1007365/2/pcbi.1007365.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210221%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210221T071950Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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 |
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