Epigenetic time travel | Research Communities by Springer Nature

The world’s museums and natural history collections contain millions of biological specimens collected over hundreds of years. Traditionally, the physical features of these specimens were used to describe species that were new to science, understand variation within and between species, and provide a physical record of global biodiversity. 
More recently, these specimens have become a resource for genetic approaches to understanding our world. Museums and collections are now at the forefront of new DNA technologies, such as assembling reference genomes and DNA sequence libraries to study how species develop and adapt over time and to conduct environmental monitoring. 

Hidden molecular treasures. Once considered devoid of sequenceable DNA, specimens such as these formalin-preserved reptiles housed in the Australian National Wildlife Collection are now valuable molecular resources.

Linking chromatin biology and museum science 
The chemical fixative formalin has long been used to preserve animal specimens, and almost exclusively so for fish and reptiles. This is the same way that tissue biopsies are preserved by pathologists in human medicine – for example when detecting skin cancers. Formalin works by creating strong molecular bonds (crosslinks) throughout biological tissues, thus preserving fine morphological features for future study. Until recently, it was assumed that this crosslinking made DNA-sequencing studies impossible. 
However, formalin treatment is a first step in many lab protocols used to study the functional 3D structure of the genome. For example, formalin is routinely used to crosslink the DNA and proteins that make up chromatin. These crosslinks freeze chromatin structure in place, thus providing a snapshot of the dynamic molecular dance chromatin undergoes to control how genes are expressed. 
Viewing formalin-preservation through this lens, we began to think of old specimens as being suspended in an assay that began many decades ago. This idea opened the opportunity to use old collections in new ways. 
Our breakthrough was realising that museum practices have unintentionally preserved detailed molecular data about how species coped with environmental change in the past. By modifying two laboratory protocols – FAIRE-Seq and MNase-Seq – we were able to study preserved museum specimens in unprecedented ways. FAIRE-Seq and MNase-Seq rely on different approaches to gain information about which genes are undergoing expression. FAIRE-Seq enriches for active DNA regions by removing the tightly bound inactive regions, while MNase-Seq enriches for nucleosome-bound DNA by breaking down the interlinking DNA thereby providing high resolution details of chromatin architecture. We optimised these techniques, which are usually applied to fresh samples, and made it possible to analyse gene expression in much older museum tissues. 
Our recent study published in Nature Communications links the disparate fields of chromatin biology and museum science to generate historical chromatin profiles from formalin-preserved archival tissues.   
In experiments with yeast and mouse models, we showed that chromatin architecture is preserved even in heavily fixed specimens. This allowed us to generate semi-quantitative estimates of relative gene expression. These chromatin profiles are reproducible, tissue-specific, sex-specific and environmental condition-dependent in vertebrate specimens, as we demonstrate in eastern water dragon (Intellegama lesueurii lesueurii) specimens collected in Queensland, Australia, as far back as 1905. 

New possibilities from old specimens. No longer a molecular roadblock, formalin preservation may in fact be the unexpected key to understanding how species adapt rapidly to environmental change by modifying their epigenome. (Left: a preserved water dragon (Intellegama lesueurii) awaiting it’s molecular moment to shine; Right: Senior author, Dr. Clare Holleley, explores the Australian National Wildlife Collection vaults with a new perspective)

Travel back in time to predict the future 
Our discovery opens the door to using formalin-fixed museum specimens to study historical gene expression and environmental impacts over the past century. This is possible because 3D chromatin structure responds to environmental pressures and controls gene expression responsible for species’ trait diversity, developmental processes, and manifestation of disease. This means our assay can provide a snapshot of how animals responded at a molecular level to past environmental events. 
When applied to specimens collected across time and space, and matched to environmental data, our chromatin assays have the potential to elucidate species’ response to environmental change. These data could be used to predict and mitigate the impacts of future environmental change, tracking historical emergence of pathogens, and studying longer-term impacts of invasive species. These historical data could form the basis for discovering new bioindicators of environmental stress and assist government and land managers to direct conservation resources most effectively.  
Flow on benefits for medical science 
Many human diseases involve complex interactions between genes and environmental factors. Heart disease, cancer and long Covid are just a few. 
Formalin-fixed paraffin-embedded (FFPE) histology samples are routinely used to study molecular drivers of human disease. Just as our methods enable reconstruction of historical chromatin profiles from museum specimens, they could be used to provide access to molecular information held in human samples beyond those captured in FFPE specimens, such as the thousands of formalin-preserved medical specimens held in tissue banks. Applied broadly to tissue specimens, our assays could deepen our understanding of how our environment and our genes affect cancer risk, the rate of ageing and the impact of infections on our body.