Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies

Abstract

Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism-wide gene expression at the time of death. While DNA methylation and RNA-Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid-preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue-specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase-seq and FAIRE-seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species.

Keywords: DNA; chromatin accessibility; epigenetics; formaldehyde; formalin‐fixed; gene expression; genome; museomics; museum; museum epigenomics.

FIGURE 1

Re‐framing formalin from DNA damage to genomic opportunity. Contrasted with the classic dogma that formalin preservation inhibits molecular interrogation, our reframed perspective highlights the potential held within formalin‐preserved museum specimens such as these emerald tree monitors ( Varanus prasinus ) collected in Papua New Guinea in 1969 (ANWC Reg no. R01048) and 1971 (ANWC Reg no. R01065). Millions of formalin‐preserved specimens, long viewed as intractable for molecular work, can now be viewed as valuable repositories of molecular data. In addition to yielding DNA sequence data, formalin‐fixed specimens preserve genome‐wide chromatin architecture. These advancements elevate the molecular potential of formalin‐fixed specimens, and their utility may one day exceed the diversity of applications currently observed for dried and ethanol‐preserved collections. Formalin‐fixed specimens are uniquely poised to enable characterisation of historical gene activity across a broad range of tissues.