Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase

• Published in: DNA research 2018-10, Vol.25 (5), p.521-533
• Main Authors: Tang, Wanxiangfu, Mun, Seyoung, Joshi, Aditya, Han, Kyudong, Liang, Ping
• Format: Article
• Language: English
• Subjects: Animals; Chromosome Mapping; DNA Transposable Elements; Evolution, Molecular; Genome, Human; Genomics - methods; Humans; Mutagenesis, Insertional; Nucleotide Motifs; Primates - genetics; Repetitive Sequences, Nucleic Acid; Reproducibility of Results
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/dsy022

Mobile elements (MEs) collectively contribute to at least 50% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition, MEs serve as a significant source for both inter- and intra-species genetic and phenotypic diversity during primate and human evolution. By making use of the most recent genome sequences for human and many other closely related primates and robust multi-way comparative genomic approach, we identified a total of 14,870 human-specific MEs (HS-MEs) with more than 8,000 being newly identified. Collectively, these HS-MEs contribute to a total of 14.2 Mbp net genome sequence increase. Several new observations were made based on these HS-MEs, including the finding of Y chromosome as a strikingly hot target for HS-MEs and a strong mutual preference for SINE-R/VNTR/Alu (SVAs). Furthermore, ∼8,000 of these HS-MEs were found to locate in the vicinity of ∼4,900 genes, and collectively they contribute to ∼84 kb sequences in the human reference transcriptome in association with over 300 genes, including protein-coding sequences for 40 genes. In conclusion, our results demonstrate that MEs made a significant contribution to the evolution of human genome by participating in gene function in a human-specific fashion.