A Preliminary Analysis Of The Impact Of Long Non-coding RNA And Epigenetic Regulation On Horse Domestication

Domestication is a special kind of evolution that benefits both of the involved species during the natural selection and co-evolution,and is the process by which the breeding of plants or animals shifts from naturally occurred to human controlled The domestication of horses,which had significantly influenced the migration of humans and the spread of human civilization,is a complex and interesting process.Domestication of horses occurred about 5500 years ago or earlier.In recent years,studies of horse domestication have mainly focused on when and how horses were domesticated.These studies are mainly about protein-coding genes.Long non-coding RNAs(lncRNAs)can recruit epigenomic modification enzymes to specific locations in the genome and therefore are key epigenetic regulators.No computational researches on the roles of horses' lncRNAs in domestication have been reported.Here we analyzed the changes of lncRNAs and their epigenetic regulation relationship during the domestication of horses.According to the GO(Gene Ontology)and KEGG(Kyoto Encyclopedia of Genes and Genomes)databases,we specifically analyzed the characteristics of target gene enrichment.We examined a wild horse that was not domesticated in 40000 BCE,a Botai horse that lived 5500 years ago,an ancient horse that was domesticated in 2300 BP,and a modern horse.We comprehensively analyzed high-quality 65 lncRNAs sequences and 22341 promoter region(+3500?-1500 TSS)sequences in these 4 horses,and found that the IncRNA sequences did not change much(in term of sequence distance).Since 58 lncRNAs had TTSs in 2289 genes,these IncRNAs and their potential target genes form a potentially complex regulatory network.TTSs show losses and gains during domestication,and the target genes in which the TTS shows binding affinity increase from wild horses to modern horses are involved in immune response and nervous system regulation.Some target genes of IncRNAs have been reported to be important for domestication.The results of our analysis support the"neural crest" hypothesis.GO and KEGG pathway enrichment analysis indicats that enriched target genes are related to olfaction and sensory stimulation,and some target genes are significantly related to metabolic pathways and neuroactive ligand-receptor interaction pathway.These results suggest that IncRNA-mediated epigenetic modification may have greatly influenced the domestication of horses.An interesting question to be further explored is whether these results are common,and whether the impact of lncRNA on domestication always focus on these pathways in the domestication of other animals.