Ancient microRNA profiles of a 14,300-year-old canid are taxonomically informative and give glimpses into gene regulation from the Pleistocene

Abstract

Ancient DNA sequencing is the key technology for paleogenomic studies and today a routine method in many laboratories. Recent analyses have shown that, under favoring conditions, also RNA can be sequenced from historical and even ancient samples. We have re-analyzed ancient RNA data from a Pleistocene canid and find -in addition to the previously described messenger RNA fragments -intact microRNAs, which are short transcripts with important gene regulatory functions. With an extraordinary age of 14,300 years, the canid microRNA profiles are the oldest ever reported. Despite their age, we show that the microRNA profiles are conclusive of taxonomic origin, tissue identity with organ-and cell-type specific signatures, and that they yield glimpses into gene regulatory activity and biological processes from the Pleistocene. In summary, we here show that straightforward microRNA analyses hold great promise for deeper insights into gene regulation in extinct animals.

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

“…High quality in silico annotation of genomes is particularly important for organisms where no RNA is likely to ever become available. This is the case for species such as mammoths that went extinct millennia or even millions of years ago (but see (Fromm et al, 2019b)). Using available data from extinct and extant elephantids (Palkopoulou et al, 2015, 2018), we ran MirMachine on 16 afrotherian genomes, including the hyrax ( Procavia capensis ) from Ensembl and the tenrec ( Echinops telfairi ) from MirGeneDB, and 14 elephantids including extant savanna elephants ( Loxodonta africana ), forest elephants ( Loxodonta cyclotis ) and asian elephants ( Elephas maximus ) respectively (Figure 6A, green elephantid silhouettes), but also extinct american mastodon ( Mammuthus americanum ), straight-tusked elephants ( Palaeoloxodon antiquus ), columbian mammoth ( Mammuthus columbi ) and the woolly mammoths ( Mammuthus primigenius ) (Figure 6A, red elephantid silhouettes).…”

“…High quality in silico annotation of genomes is particularly important for organisms where no RNA is likely to ever become available. This is the case for species such as mammoths that went extinct millennia or even millions of years ago (but see (Fromm et al, 2019b)).…”