Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast

Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. Here we cultured yeast (Saccharomyces cerevisiae) under normal and heat-shock conditions then fixed the cells with formalin for 15 minutes, 1 hour, 6 hours, and 24 hours. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and enables semi-quantitative estimates of relative gene expression in this yeast model.福尔马林可使受其作用的细胞内形成分子间与分子内交联。该交联特性可用于表征染色质状态，正如FAIRE（甲醛辅助分离调控元件，Formaldehyde-Assisted Isolation of Regulatory Elements）实验与MNase（微球菌核酸酶，micrococcal nuclease）实验所采用的方法。本研究团队旨在优化上述实验方法，以应用于博物馆馆藏经福尔马林处理的标本。为此，我们首先探究了延长福尔马林固定时间对FAIRE与MNase处理后产生的测序读段比对特征的影响。本研究将酿酒酵母（Saccharomyces cerevisiae）分别在正常培养与热激条件下培养，随后用福尔马林固定细胞，固定时长分别为15分钟、1小时、6小时与24小时。我们发现，高强度福尔马林固定并不会消除染色质开放差异的特征，反而会对其进行调控，并且可在该酵母模型中实现相对基因表达的半定量估算。