Figure 1. Transposable Elements in the Human Genome.

Panel A shows protein-coding exons and classes of human transposable elements as a percentage of the genome.¹ As shown in Panel B, DNA transposons encode transposase, an enzyme that binds at or near inverted repeats flanking the element (white arrows flanking transposase) to promote mobility by means of a cut-and-paste mechanism.⁶ Retrotransposons mobilize by means of a copy-and-paste mechanism through an RNA intermediate.⁷ Human endogenous retroviruses (HERVs) contain sequences analogous to the gag, pol, and env genes of retroviruses, but most HERVs, if not all of them, are not active in humans.⁸ Elements are considered to be autonomous when they encode the protein activities necessary for retrotransposition (e.g., an endonuclease [EN] and a reverse transcriptase [RT]). The arrow at the 5′ end of poly(A) retrotransposons denotes the transcription start site from their internal promoter. Nonautonomous elements do not encode proteins; their retrotransposition depends on the proteins encoded by autonomous elements.⁹ Nonautonomous elements include Alu elements and SVAs. Alu elements have a size of approximately 280 bp and consist of two monomers separated by an adenosine-rich (AR) linker; the left Alu monomer has an internal RNA polymerase III promoter (bars labeled A and B). SVAs are composite elements with a portion of a HERV (SINE-R [short interspersed element of HERV origin]), a variable number of tandem repeats (VNTRs), and a backward Alu, as well as a CCCTCT multimer. Processed pseudogenes are copies of cellular messenger RNAs that have been reverse-transcribed into DNA and lack introns. C denotes cysteine-rich domain (encoded by ORF2), HERV-K a HERV of the K type, LINE long interspersed element, LTR long terminal repeat, ORF1 open reading frame 1, ORF2 open reading frame 2, and UTR untranslated region. The diagram in Panel B is adapted from Beck et al.¹⁰