Prospects for analyzing ancient RNA in preserved materials

Abstract

An ever increasing wealth of ancient biological material is providing opportunities to study biomolecules. Animal, plant, and microbial samples dating back hundreds, thousands, and even millions of years have been preserved in a dry state under climatic conditions ranging from the arctic to hot deserts. Various small molecules, often crystalized or polymerized, have improved preservation. Modern methods such as polymerase chain reaction (PCR), mass spectrometry, and shotgun sequencing have detected and characterized ancient biomolecules. Modern sequencing has the capacity not only to assemble the whole genome of the target host but also those of the host's parasites, mutualists, and commensals. The study of ancient RNA has barely begun. Several studies show that RNA has been preserved for decades to hundreds of years and the germination of ancient seeds implies that messenger RNA can be preserved for thousands of years. This review briefly examines the types of ancient materials available and assesses their suitability for the study of ancient RNA. Sequencing RNA from this material has the potential not only to illuminate the target host's transcriptome and small RNAs but also to characterize the host's RNA parasites: viruses and viroids.

Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970’s Egypt

“…The remaining pupae were freeze-dried and stored at room temperature during the following decades. Drying is a well-established method for the long-term preservation of virus samples, allowing the recovery of live virus even from centuries-old herbarium specimens [ 17 , 26 ].…”

Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens

“…Ancient RNA techniques, particularly when isolating RNA from sources other than "wet" tissue, are still under development. However, remarkable results, including the sequences of RNA virus genomes from 750-1000 years old grains and maize cobs, have already been published [179,[187][188][189]. Human genomes from all over the world show strong selective sweeps resulting from extensive adaptations to RNA virus infections, suggesting that this class of pathogens was as important in past epidemics as it is now [190].…”

“…As their graves in Buckden, Cambridgeshire, England, are still there, the remains could possibly be subjected to ancient DNA analysis. However, current techniques are not optimized yet for ancient RNA analysis from bone or teeth [179], should sweating disease have been caused by an RNA virus. In contrast to most rhabdoviruses, tibroviruses are able to cause a viremia, allowing them in theory to be isolated from dental pulp.…”

Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels

“…The successful purification of ancient RNA, including that from microbial origin, has been described, although not many studies are yet available. The most common case of recovery and analysis of ancient microbial RNA is that of viruses and viroids from ancient samples that had been preserved chemically, frozen or in a dry state ( Guy, 2014 ; Smith et al, 2014 ). For instance, the RNA virus causing the 1918 great influenza could be isolated from formalin-fixed, paraffin-embedded, lung autopsy materials using proteinase K digestion, followed by either a phenol-chloroform or an acidic guanidinium thiocyanate-phenol chloroform extraction step, and isopropanol precipitation in the presence of glycogen ( Krafft et al, 1997 ).…”