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Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models
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| Title: | Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models |
| Authors: | Takasuka, Taichi E. Browse this author | | Stein, Arnold Browse this author |
| Issue Date: | 11-May-2010 |
| Publisher: | Oxford University Press |
| Journal Title: | Nucleic Acids Research |
| Volume: | 38 |
| Issue: | 17 |
| Start Page: | 5672 |
| End Page: | 5680 |
| Publisher DOI: | 10.1093/nar/gkq279 |
| Abstract: | Abstract: Several periodic motifs have been implicated in facilitating the bending of DNA around the histone core of the nucleosome. For example, di-nucleotides AA/TT/TA and GC at ∼10-bp periods, but offset by 5 bp, are found with higher-than-expected occurrences in aligned nucleosomal DNAs in vitro and in vivo. Additionally, regularly oscillating period-10 trinucleotide motifs non-T, A/T, G and their complements have been implicated in the formation of regular nucleosome arrays. The effects of these periodic motifs on nucleosome formation have not been systematically tested directly by competitive reconstitution assays. We show that, in general, none of these period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation. The influence of periodic TAs on nucleosome formation is appreciable; with some of the 200-bp DNAs out-competing bulk nucleosomal DNA by more than 400-fold. Only the nucleotides immediately flanking TA influence its nucleosome-forming ability. Period-10 TA, when flanked by a pair of permissive nucleotides, facilitates DNA bending through compression of the minor groove. The free energy change for nucleosome formation decreases linearly with the number of consecutive TAs, up to eight. We suggest how these data can be reconciled with previous findings. |
| Rights: | © The Author(s) 2010. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. | | http://creativecommons.org/licenses/by-nc/2.5 |
| Type: | article |
| URI: | http://hdl.handle.net/2115/68278 |
| 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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