Chen Ruo-Wen, Stoeber Shane D, Nodelman Ilana M, Chen Hengye, Yang Lloyd, Bowman Gregory D, Bai Lu, Poirier Michael G
Ohio State Biochemistry Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
bioRxiv. 2025 Jan 18:2025.01.17.633597. doi: 10.1101/2025.01.17.633597.
Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from . We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences, and the rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.
核小体重新定位对于建立核小体缺失区域（NDRs）以启动转录至关重要。这个过程已经通过结构、生化和单分子方法进行了广泛研究，这些方法需要均匀定位的核小体。这通常使用维登601序列来实现，它是一种高效的核小体定位元件（NPE），因其与H3-H4组蛋白四聚体异常强的结合而被选择。由于601的人为性质，需要天然NPE来探索DNA序列在核小体重新定位中的作用。在这里，我们表征了一组来自酵母的天然核小体（YNNs）的位置分布和核小体形成自由能。我们表明，这些天然NPE可用于转录因子（TFs）和染色质重塑因子Chd1对核小体重新定位的生化研究。TFs可以直接重新定位一部分含有天然NPE的核小体，但不能重新定位含有601的核小体。相比之下，601和天然NPE序列的部分解旋相似，Chd1依赖ATP的重塑速率在601核小体快速和慢速方向的范围内。这组天然NPE为601 NPE提供了一种替代方案，可用于探测含有天然DNA序列的核小体的重新定位。
