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 must first 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. At pre-determined fixation timepoints (15min, 1 hour, 6 hours and 24 hours), we removed aliquots of fixed cells and processed them through FAIRE and MNase protocols optimised for heavily fixed yeast cells. Alongside these samples, we collected genomic DNA and RNA from both regular and heat-shocked cultures prior to fixation. The DNA samples were prepared for sequencing using an IDT xGEN Prism library kit and sequenced on a NovaSeq S4 100bp PE flowcell.