Ancient RNA

  • Oliver SmithEmail author
  • M. Thomas P. Gilbert
Part of the Population Genomics book series (POGE)


Compared to other ancient biomolecules such as DNA and proteins, ancient RNA is arguably the least studied. The reasons behind this are largely based on a relative lack of surviving material due to RNA’s molecular properties. Increasingly powerful and sensitive molecular methods however now allow for trace amounts of ancient RNA to be sequenced, to previously unthinkable depths, and doing so has made available a previously untapped layer of -omic information. It is becoming possible to ascertain the activity of an ancient genome in vivo, and thus assess environmental stresses and pathogen interaction, and uncover further epigenomic mechanisms. In this chapter we will explore the past, present, and future applications of the new paleotranscriptomics.


Adaptation aDNA Ancient RNA aRNA Environmental stress Genome regulation In vivo miRNA Paleotranscriptomics RdDM Ribosome RNA virus RNase siRNA 


  1. Allaby RG, et al. Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philos Trans R Soc Lond B Biol Sci. 2015;370(1660):20130377.PubMedPubMedCentralCrossRefGoogle Scholar
  2. Awano N, Inouye M, Phadtare S. RNase activity of polynucleotide phosphorylase is critical at low temperature in Escherichia coli and is complemented by RNase II. J Bacteriol. 2008;190(17):5924–33.PubMedPubMedCentralCrossRefGoogle Scholar
  3. Bos KI, et al. Parallel detection of ancient pathogens via array-based DNA capture. Philos Trans R Soc Lond B Biol Sci. 2015;370(1660):20130375.PubMedPubMedCentralCrossRefGoogle Scholar
  4. Briggs AW, et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A. 2007;104(37):14616–21.PubMedPubMedCentralCrossRefGoogle Scholar
  5. Briggs AW, et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2010;38(6):e87.PubMedCrossRefGoogle Scholar
  6. Brown TA, et al. Recent advances in ancient DNA research and their implications for archaeobotany. Veg Hist Archaeobotany. 2015;24(1):207–14.CrossRefGoogle Scholar
  7. Castello DJ, et al. Detection of tomato mosaic tobamovirus RNA in ancient glacial ice. Polar Biol. 1999;22(3):207–12.CrossRefGoogle Scholar
  8. Chomczynski P, Sacchi N. The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc. 2006;1(2):581–5.PubMedCrossRefGoogle Scholar
  9. Cooper A, Poinar HN. Ancient DNA: do it right or not at all. Science. 2000;289(5482):1139.PubMedCrossRefGoogle Scholar
  10. Dabney J, et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci. 2013;110(39):15758–63.PubMedCrossRefGoogle Scholar
  11. de los Rios A, Ramirez R, Estévez P. RNase in Lasallia hispanica and Cornicularia normoerica: multiplicity of electromorphs and activity changes during a hydration-dehydration cycle. J Exp Bot. 1996;47(12):1927–33.CrossRefGoogle Scholar
  12. Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 2001;15(2):188–200.PubMedPubMedCentralCrossRefGoogle Scholar
  13. Evin A, et al. Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania. Philos Trans R Soc Lond B Biol Sci. 2015;370(1660):20130616.PubMedPubMedCentralCrossRefGoogle Scholar
  14. Fabre A-L, et al. An efficient method for long-term room temperature storage of RNA. Eur J Hum Genet. 2014;22(3):379–85.PubMedCrossRefGoogle Scholar
  15. Fordyce SL, et al. Deep Sequencing of RNA from ancient maize kernels. PLoS One. 2013a;8(1):e50961.PubMedPubMedCentralCrossRefGoogle Scholar
  16. Fordyce SL, et al. Long-term RNA persistence in postmortem contexts. Investig Genet. 2013b;4(1):7.PubMedPubMedCentralCrossRefGoogle Scholar
  17. Fraile A, et al. A century of tobamovirus evolution in an Australian population of Nicotiana glauca. J Virol. 1997;71(11):8316–20.PubMedPubMedCentralGoogle Scholar
  18. Fu Q, et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature. 2014;514(7523):445–9.PubMedPubMedCentralCrossRefGoogle Scholar
  19. Ginolhac A, et al. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011;27(15):2153–5.PubMedCrossRefGoogle Scholar
  20. Guy PL. Ancient RNA? RT-PCR of 50-year-old RNA identifies peach latent mosaic viroid. Arch Virol. 2013;158(3):691–4.CrossRefGoogle Scholar
  21. Hanghøj K, et al. Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Mol Biol Evol. 2016;33:3284–98.PubMedPubMedCentralCrossRefGoogle Scholar
  22. Hansen AJ, et al. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics. 2006;173(2):1175–9.PubMedPubMedCentralCrossRefGoogle Scholar
  23. Harris ME, Christian EL. RNA crosslinking methods. Methods Enzymol. 2009;468:127–46.PubMedPubMedCentralCrossRefGoogle Scholar
  24. Higuchi R, et al. DNA sequences from the quagga, an extinct member of the horse family. Nature. 1984;312(5991):282–4.CrossRefGoogle Scholar
  25. Hofreiter M, et al. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001;29(23):4793–9.PubMedPubMedCentralCrossRefGoogle Scholar
  26. Huang Y, Li L. DNA crosslinking damage and cancer – a tale of friend and foe. Transl Cancer Res. 2013;2(3):144–54.PubMedPubMedCentralGoogle Scholar
  27. Hussain S, et al. Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol. 2013;14(11):215.PubMedPubMedCentralCrossRefGoogle Scholar
  28. Huynen L, Millar CD, Lambert DM. Resurrecting ancient animal genomes: The extinct moa and more. BioEssays. 2012;34(8):661–9.PubMedCrossRefGoogle Scholar
  29. Keller A, et al. miRNAs in ancient tissue specimens of the Tyrolean Iceman. Mol Biol Evol. 2017;34:793–801.PubMedGoogle Scholar
  30. Kistler L, Ware R, Smith O, Collins MJ, Allaby RG. A new general model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res. 2017;45(11):6310–20.PubMedPubMedCentralCrossRefGoogle Scholar
  31. Laing LG, Draper DE. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J Mol Biol. 1994;237(5):560–76.PubMedCrossRefGoogle Scholar
  32. Lindahl T. Irreversible heat inactivation of transfer ribonucleic acids. J Biol Chem. 1967;242(8):1970–3.PubMedGoogle Scholar
  33. Meyer M, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012;338(6104):222–6.PubMedPubMedCentralCrossRefGoogle Scholar
  34. Mouttham N, et al. Surveying the repair of ancient DNA from bones via high-throughput sequencing. BioTechniques. 2015;59(1):19.PubMedCrossRefGoogle Scholar
  35. Müller R, Roberts CA, Brown TA. Biomolecular identification of ancient Mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe. Am J Phys Anthropol. 2014;153(2):178–89.PubMedCrossRefGoogle Scholar
  36. Ng TFF, et al. Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch. Proc Natl Acad Sci. 2014;111(47):16842–7.PubMedCrossRefGoogle Scholar
  37. Orlando L, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 2013;499(7456):74–8.CrossRefGoogle Scholar
  38. Pääbo S. Molecular genetic investigations of ancient human remains. Cold Spring Harb Symp Quant Biol. 1986;51:441–6.PubMedCrossRefGoogle Scholar
  39. Pääbo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci U S A. 1989;86(6):1939–43.PubMedPubMedCentralCrossRefGoogle Scholar
  40. Palmer SA, et al. Archaeogenomic evidence of punctuated genome evolution in Gossypium. Mol Biol Evol. 2012;29(8):2031–8.CrossRefGoogle Scholar
  41. Paris HS. Overview of the origins and history of the five major cucurbit crops: issues for ancient DNA analysis of archaeological specimens. Veg Hist Archaeobotany. 2016;25:405–14.CrossRefGoogle Scholar
  42. Pinhasi R, et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One. 2015;10(6):e0129102.PubMedPubMedCentralCrossRefGoogle Scholar
  43. Poeckh T, et al. Adsorption and elution characteristics of nucleic acids on silica surfaces and their use in designing a miniaturized purification unit. Anal Biochem. 2008;373(2):253–62.PubMedCrossRefGoogle Scholar
  44. Renaud G, et al. gargammel: a sequence simulator for ancient DNA. Bioinformatics. 2017;33:577–9.PubMedGoogle Scholar
  45. Rogan PK, Salvo JJ. Study of nucleic acids isolated from ancient remains. Am J Phys Anthropol. 1990;33(S11):195–214.CrossRefGoogle Scholar
  46. Rogers SO, Bendich AJ. Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Plant Mol Biol. 1987;9(5):509–20.PubMedCrossRefGoogle Scholar
  47. Rollo F. Characterisation by molecular hybridization of RNA fragments isolated from ancient (1400 B.C.) seeds. Theor Appl Genet. 1985;71(2):330–3.PubMedCrossRefGoogle Scholar
  48. Rollo F, Venanzi FM, Amici A. Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize. Genet Res. 1991;58(3):193–201.PubMedCrossRefGoogle Scholar
  49. Rollo F, Venanzi FM, Amici A. DNA and RNA from ancient plant seeds. In: Herrmann B, Hummel S, editors. Ancient DNA: recovery and analysis of genetic material from paleontological, archaeological, museum, medical, and forensic specimens. New York: Springer; 1994. p. 218–36.CrossRefGoogle Scholar
  50. Sallon S, et al. Germination, genetics, and growth of an ancient date seed. Science. 2008;320(5882):1464.PubMedCrossRefGoogle Scholar
  51. Schaefer M, et al. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res. 2009;37(2):e12.PubMedCrossRefGoogle Scholar
  52. Schuenemann VJ, et al. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc Natl Acad Sci. 2011;108(38):E746–52.PubMedCrossRefGoogle Scholar
  53. Seguin-Orlando A, et al. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science. 2014;346(6213):1113–8.CrossRefGoogle Scholar
  54. Skoglund P, et al. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol. 2015;25(11):1515–9.PubMedCrossRefGoogle Scholar
  55. Smith O. Small RNA-mediated regulation, adaptation and stress response in barley archaeogenome. PhD thesis, School of Life Sciences, University of Warwick; 2012.Google Scholar
  56. Smith O, et al. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus. Sci Rep. 2014a;4:4003.PubMedPubMedCentralCrossRefGoogle Scholar
  57. Smith O, et al. Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep. 2014b;4:5559.PubMedPubMedCentralCrossRefGoogle Scholar
  58. Smith O, et al. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science. 2015;347(6225):998–1001.CrossRefGoogle Scholar
  59. Smith O, et al. Small RNA activity in archaeological barley shows novel germination inhibition in response to environment. Mol Biol Evol. 2017;34(10):2555–62.PubMedPubMedCentralCrossRefGoogle Scholar
  60. Snead NM, Rossi JJ. Biogenesis and function of endogenous and exogenous siRNAs. Wiley Interdiscip Rev RNA. 2010;1(1):117–31.PubMedCrossRefGoogle Scholar
  61. Spanò C, Buselli R, Grilli I. Dormancy and germination in wheat embryos: ribonucleases and hormonal control. Biol Plant. 2008;52(4):660.CrossRefGoogle Scholar
  62. Squires JE, et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 2012;40(11):5023–33.PubMedPubMedCentralCrossRefGoogle Scholar
  63. Stahl EA, Bishop JG. Plant-pathogen arms races at the molecular level. Curr Opin Plant Biol. 2000;3(4):299–304.PubMedCrossRefGoogle Scholar
  64. Sutton DH, Brown T. The dependence of DNase I activity on the conformation of oligodeoxynucleotides. Biochem J. 1997;321(2):481–6.PubMedPubMedCentralCrossRefGoogle Scholar
  65. Tuschl T, et al. Modified RNA ligase for efficient 3′ modification of RNA. Google Patents; 2014.Google Scholar
  66. Venanzi FM, Rollo F. Mummy RNA lasts longer. Nature. 1990;343(6253):25–6.PubMedCrossRefGoogle Scholar
  67. Vernot B, Akey JM. Complex history of admixture between modern humans and Neandertals. Am J Hum Genet. 2015;96(3):448–53.PubMedPubMedCentralCrossRefGoogle Scholar
  68. Willerslev E, Cooper A. Review paper. Ancient DNA. Proc R Soc B Biol Sci. 2005;272(1558):3–16.CrossRefGoogle Scholar
  69. Willerslev E, Hansen AJ, Poinar HN. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol. 2004;19(3):141–7.CrossRefGoogle Scholar
  70. Winter J, et al. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol. 2009;11(3):228–34.PubMedCrossRefGoogle Scholar
  71. Worobey M. Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus. J Virol. 2008;82(7):3769–74.PubMedPubMedCentralCrossRefGoogle Scholar
  72. Yashina S, et al. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. Proc Natl Acad Sci U S A. 2012;109(10):4008–13.PubMedPubMedCentralCrossRefGoogle Scholar
  73. Zhang G, et al. Evidence of influenza A virus RNA in Siberian lake ice. J Virol. 2006;80(24):12229–35.PubMedPubMedCentralCrossRefGoogle Scholar
  74. Zuker M, Mathews DH, Turner DH. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J, Clark BFC, editors. RNA biochemistry and biotechnology. Dordrecht: Springer; 1999. p. 11–43.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  1. 1.School of Life SciencesUniversity of WarwickCoventryUK
  2. 2.Centre for GeoGeneticsNatural History Museum of Denmark, University of CopenhagenCopenhagenDenmark
  3. 3.Norwegian University of Science and Technology, University MuseumTrondheimNorway

Personalised recommendations