A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The -end sequences of various SINEs originated from a corresponding LINE. As the -untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the -end sequence of the RNA template. However, the -ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of -poly(A) repeats. Since the -poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. 1. RNA-Mediated Gene Duplication and Retroposons 1.1. Retrogenes and Processed Pseudogenes Gene duplication is a fundamental process of gene evolution [1]. There are two types of gene duplication: direct duplication of genomic DNA and retropositional events [2–4]. Processed pseudogenes (PPs) are reverse-transcribed intronless cDNA copies of mRNA that have been reinserted into the genome (Figure 1) [5, 6]; they are especially abundant in mammalian genomes [7, 8]. PPs are not usually transcribed because they lack an external promoter; therefore, they have long been viewed as evolutionary dead ends with little biological relevance. However, recent studies have unveiled a substantial number of “processed genes” or “retrogenes” with novel functions that are derived from the mRNA of various intron-containing genes [9–12]. Molecular biological studies showed that a class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been involved in the reverse transcription of nonautonomous retroposons, such as PPs (retrogenes) and short interspersed elements (SINEs) [13]. Figure 1: Schematic representation of the formation of a processed pseudogene. 1.2. Retroposons Eukaryotic genomes generally contain an extraordinary number of
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