Biology Reference
In-Depth Information
Although all TEs are frequently considered to have a parasitic aspect, the
nonautonomous group of non-LTR transposons, such as SINEs (represented by
Alu elements in the primate lineage) and SVA (hominoid-specific retroele-
ments) take this parasitism to a another level. Because SINEs and SVA elements
do not encode any proteins for orchestrating their own mobilization (hence the
“nonautonomous”) they have evolved to parasitize the retrotransposition ma-
chinery of the currently active human autonomous non-LTR retroelement,
LINE-1. The retrotransposition process of non-LTR retrotransposons begins
with transcription of a retrotranspositionally competent locus within the host
genome. L1, Alu, and SVA elements accumulated in the human genome to
500,000, 1,000,000, and 1700 copies, respectively, the majority of which are
inactive (Lander
, 2001). Out of the structurally intact TE copies only a
fraction of loci retained functional promoters. Finally, a large proportion of the
potentially expressed loci have lost the ability to mobilize due to mutations
inactivating functional protein domains or sequences within their RNAs critical
for amplification. The former applies only to L1 elements (because only they
encode proteins), while the latter is true for all human retrotransposons. As a
result there are about 100 predicted active L1 loci per haploid human genome
(Penzkofer
et al.
, 2005). L1 elements are transcribed by an atypical bidirectional
internal RNA Pol-II promoter located within the L1 5
0
untranslated region,
5
0
UTR (Speek, 2001; Swergold, 1990). At least some of the produced L1
mRNAs are capped and RNA capping is reported to stimulate translation of
L1 proteins (Dmitriev
et al.
, 2007; Kulpa and Moran, 2005; McMillan and
Singer, 1993). As a result of Pol-II transcription, L1 mRNAs are polyadenylated.
The presence of this polyA tail at the 3
0
end is critical for the L1 integration
process (Symer
et al.
, 2002).
Very little is known about transcription of SVA elements. They are
most likely transcribed by RNA Pol-II because of the presence of multiple RNA
Pol-III terminators within their sequence and evidence for posttranscriptional
processing of SVA RNA characteristic of the Pol-II generated RNAs (Damert
et al.
et al.
, 2005).
Bioinformatic analysis of SVA elements identified in the human genome, fol-
lowed by empirical testing, suggested that SVA retrotransposons do not contain
an internal promoter that can be carried over into the new genomic location to
ensure efficient transcription of the
, 2009; Hancks
et al.
, 2009; Ostertag
et al.
, 2003; Wang
et al.
, 2009). SVA
loci appear to rely on the existence of the functional promoters at the sites of
their integration (Damert
de novo
insertions (Damert
et al.
, 2009). Along with their relatively recent
appearance on the evolutionary scene, the lack of a mobile promoter may
explain their relatively low copy numbers.
In contrast to L1 and SVA elements, Alu transcription is carried out by
the RNA Pol-III complex as is the case with its 7SLRNA ancestor. Alu RNA is
not capped and the artificial generation of
et al.
the capped Alu transcripts
