Nonltr Retrotransposons

Non-long terminal repeat (LTR) retrotransposons are the most abundant repetitive elements in human genomic DNA and represent approx one-third of the genome (Table 1). Their DNA copies are co-linear with the RNA transcripts and they lack LTRs present in retroviruses. Autonomous non-LTR retrotransposons are often referred to as LINEs and their nonautono-mous counterparts as SINEs. The human genome contains two superfamilies of LINEs: active L1 (LINE1) elements, and extinct families of L2 and L3 elements (Table 1). The latter belong to the CR1 superfamily. Human SINEs are represented by the active Alu and SVA repeats retrotransposed by L1 elements, and by the extinct mammalian-wide interspersed repeat (MIR) and MIR3 SINEs that coamplified with L2 and L3 families, respectively. Active L1, Alu and SVA non-LTR retrotransposons are described in Chapters 2 and 3. Here, we concentrate on ancient LINE (see Ancient LINEs) and SINE (see Ancient SINEs) elements. We also review L1-retroposed copies of cellular transcripts known as processed pseudogenes (see Processed Pseudogenes).

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