Additionally, there is a second class of parasitic element found in hominid primates, designated SVA, which is much less well understood and remains difficult to categorize according to existing schemes due to its chimeric nature (Fig. LINE-1 elements are composed of the 5′ UTR that contains an internal RNA polymerase II (pol II) promoter (PRO) and two open reading frames (ORF1 and ORF2) that are separated in mouse and human L1s but are overlapping in the rat LINE-1.Adjacent to ORF2 is the 3′ UTR that contains a polyadenylation (p A) signal and ends in a stretch of adenine residues (p A tail) of variable length.
2006), and the creation of new varieties of grapes with altered pigmentation (Kobayashi et al. There is also an example of a SVA element carrying downstream genic sequences to new locations, generating a new functional gene family (Xing et al. As we discuss below, these and other such discoveries have resulted in a shift for some authors from the characterization of TEs as primarily “parasitic” to one wherein TEs are more or less cultivated in the genome for their beneficial possibilities.
L1 transcription, which is driven by an unconventional RNA polymerase II promoter residing in the beginning of the 5′ untranslated region (UTR) (Swergold 1990; Severynse et al.
1992), is influenced by the upstream genomic sequences (Lavie et al. The presence of the L1 promoter within the RNA coding region is reminiscent of an RNA polymerase III promoter (Kurose et al. However, its length, coding capacity, and processing are strong indicators that RNA polymerase II is the primary vehicle for L1 expression.
With rare exception, transposable elements (TEs) comprise a significant fraction of all eukaryotic organisms for which appreciable genomic sequence is available. 2006, and are therefore not covered extensively in this review).
As more genomes are sequenced, we are uncovering an ever-increasing diversity of mobile element families as well as a remarkable level of variation in the overall fraction of genomes occupied by these elements. Only recently, a third class of autonomous elements, RTE (Fig. In addition to autonomous non-LTR elements, mammalian genomes also contain a number of highly successful parasites of L1 elements, referred to as short interspersed elements (SINEs).