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Sequence Information Encoded in DNA that May Influence Long-Range Chromatin Structure Correlates with Human Chromosome Functions
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| Title: | Sequence Information Encoded in DNA that May Influence Long-Range Chromatin Structure Correlates with Human Chromosome Functions |
| Authors: | Takasuka, Taichi E. Browse this author | | Cioffi, Alfred Browse this author | | Stein, Arnold Browse this author |
| Issue Date: | 9-Jul-2008 |
| Publisher: | The Public Library of Science (PLoS) |
| Journal Title: | PLoS ONE |
| Volume: | 3 |
| Issue: | 7 |
| Start Page: | e2643 |
| Publisher DOI: | 10.1371/journal.pone.0002643 |
| Abstract: | Abstract: Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG) existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y). Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions ≥300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (≥300 kb) genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function. |
| Rights: | © 2008 Takasuka et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | | https://creativecommons.org/licenses/by/4.0/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/68284 |
| Appears in Collections: | 農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 高須賀 太一
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