Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan.
Department of Viticulture and Enology, University of California, Davis, Davis, California, United States of America.
PLoS One. 2020 Nov 12;15(11):e0242348. doi: 10.1371/journal.pone.0242348. eCollection 2020.
Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.
染色质结构，包括核小体定位，通过影响蛋白质-DNA 相互作用，在转录调控中起着至关重要的作用。已知 DNA 拓扑结构会影响染色质结构，并且在这样做的过程中，也可以改变转录。然而，将转录调控事件与受 DNA 拓扑结构变化调控的染色质结构联系起来的详细机制仍有待充分定义。在这里，我们证明裂殖酵母 fbp1 和 prp3 基因的核小体定位和转录输出会被拓扑异构酶活性的增加所改变。考虑到长非编码 RNA (lncRNA) 是从 fbp1 的上游区域转录而来，并且对 fbp1 基因的表达很重要，我们假设拓扑异构酶活性引起的 DNA 拓扑状态的局部变化可能会改变 lncRNA 和 fbp1 的转录。支持这一点，我们发现拓扑异构酶的过表达导致 fbp1 启动子区域内定位核小体的不稳定性，这伴随着 fbp1 转录的异常。同样，拓扑异构酶的直接募集，而不是无催化活性的形式，到 fbp1 的启动子区域导致核小体定位的局部变化，也伴随着 fbp1 转录的改变。这些数据表明，拓扑异构酶活性诱导的 DNA 拓扑状态的变化可能通过调节核小体定位导致 fbp1 转录的改变。
