Human transposable elements in Repbase: genomic footprints from fish to humans

Abstract

Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades (L1, CR1, L2, Crack, RTE, RTEX, R4, Vingi, Tx1 and Penelope) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (SINE1/7SL, SINE2/tRNA, and SINE3/5S) of short interspersed elements (SINEs), 1 composite retrotransposon (SVA) family, 5 classes (ERV1, ERV2, ERV3, Gypsy and DIRS) of LTR retrotransposons, and 12 superfamilies (Crypton, Ginger1, Harbinger, hAT, Helitron, Kolobok, Mariner, Merlin, MuDR, P, piggyBac and Transib) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome.

Keywords: Crypton; DNA transposons; Human repeat; LTR retrotransposons; MER; Non-LTR retrotransposons; Repbase; SINE; Transposable elements; UCON.

Fig. 1

Nucleotide sequence alignments of ancient repeats with characterized TEs. Nucleotides identical to the uppermost sequence are shaded. Numbers in parentheses indicate the nucleotide position in the consensus. a UCON82 is an RTE non-LTR retrotransposon family. b UCON39 is an ancient Mariner DNA transposon family. c Eulor5 and Eulor6 are ancient Crypton DNA transposon families