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Abstract Short interspersed elements (SINEs) are mobile genetic elements that invade the genomes of many eukaryotes. Since their discovery about 30 years ago, many gaps in our understanding of the biology and function of SINEs have been filled. This review summarizes the past and recent advances in the studies of SINEs. The structure and origin of SINEs as well as the processes involved in their amplification, transcription, RNA processing, reverse transcription, and integration of a SINE copy into the genome are considered. Then we focus on the significance of SINEs for the host genomes. While these genomic parasites can be deleterious to the cell, the long‐term being in the genome has made SINEs a valuable source of genetic variation providing regulatory elements for gene expression, alternative splice sites, polyadenylation signals, and even functional RNA genes. WIREs RNA 2011 2 772–786 DOI: 10.1002/wrna.91 This article is categorized under: RNA Processing > Processing of Small RNAs RNA in Disease and Development > RNA in Development

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Short interspersed element (SINE) structure examples. (a) CAN, tRNA‐derived SINE with a unique region of unknown origin and a (TC)n stretch; (b) Ther‐1, tRNA‐derived SINE with a CORE domain and a LINE‐derived region; (c) Opo‐1, tRNA‐derived SINE with a CORE domain and a unique region; (d) Ped‐2, tRNA‐derived SINE with a bipartite LINE‐derived region; (e) ID, simple tRNA‐derived SINE; (f) Lun‐1, tRNA‐derived SINE with a V‐domain, a (TG)n stretch, and a unique region; (g) B1, 7SL RNA‐derived SINE with an internal duplication; (h) MEG‐RL, 5S rRNA‐derived SINE with a unique region; (i) MEN, dimeric tRNA/7SL RNA‐derived SINE. Boxes with dotted background correspond to pol III promoter regions; ‘???’ corresponds to body parts of unknown origin; direct repeats including terminal target site duplications are indicated by arrows.

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Length distribution for 122 eukaryotic short interspersed elements (without tail).

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Short interspersed element (SINE) life cycle. (a) Schematic amplification cycle. (b) Target‐primed reverse transcription of SINEs. LINE, long interspersed element; pol III, RNA polymerase III; RT, reverse transcriptase; TSD, target site duplication.

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Transcription of T+ and T short interspersed elements. T, transcription termination signal; pA, polyadenylation signal.

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Occurrence of short interspersed element structures. tRNA is tRNA‐derived head; ??? corresponds to body parts of unknown origin; CORE is CORE, Deu, V, or Ceph domains; LINE is long interspersed element‐derived body region; and ‘∼∼∼’ denotes the tail.

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