Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America.
Qubit Software LLC, Spanish Fork, Utah, United States of America.
PLoS One. 2021 Oct 21;16(10):e0258737. doi: 10.1371/journal.pone.0258737. eCollection 2021.
The most basic level of eukaryotic gene regulation is the presence or absence of nucleosomes on DNA regulatory elements. In an effort to elucidate in vivo nucleosome patterns, in vitro studies are frequently used. In vitro, short DNA fragments are more favorable for nucleosome formation, increasing the likelihood of nucleosome occupancy. This may in part result from the fact that nucleosomes prefer to form on the terminal ends of linear DNA. This phenomenon has the potential to bias in vitro reconstituted nucleosomes and skew results. If the ends of DNA fragments are known, the reads falling close to the ends are typically discarded. In this study we confirm the phenomenon of end bias of in vitro nucleosomes. We describe a method in which nearly identical libraries, with different known ends, are used to recover nucleosomes which form towards the terminal ends of fragmented DNA. Finally, we illustrate that although nucleosomes prefer to form on DNA ends, it does not appear to skew results or the interpretation thereof.
真核生物基因调控的最基本层次是 DNA 调控元件上核小体的存在或缺失。为了阐明体内核小体模式,经常使用体外研究。在体外,短的 DNA 片段更有利于核小体的形成,增加核小体占据的可能性。这可能部分是由于核小体更喜欢在线性 DNA 的末端形成。这种现象有可能使体外重建的核小体产生偏差,并使结果产生偏差。如果知道 DNA 片段的末端,则通常会丢弃靠近末端的读取。在这项研究中,我们证实了体外核小体的末端偏倚现象。我们描述了一种方法,其中使用具有不同已知末端的几乎相同的文库来回收在碎片化 DNA 的末端形成的核小体。最后,我们说明尽管核小体更喜欢在 DNA 末端形成,但它似乎不会使结果或对其的解释产生偏差。