270
Anthology of Human Repetitive DNA
the non-LTR retrotransposons, they are
by far the most diverse and complex TEs
harbored by our genome. Approximately
200 families of LTR retrotransposons have
been identiFed in the human genome. A
vast majority of them were identiFed and
reconstructed using computer-assisted se-
quence analysis.
On the basis of the similarities to known
animal exogenous retroviruses, all LTR
retrotransposons present in the human
genome can be divided into three classes
(Table 3).
Class I non-LTR retrotransposons are
similar to gamma retroviruses including
mammalian type C retroviruses such
as murine leukemia virus (MLV). All
elements from this class are flanked by
4- and 5-bp TSDs that are generated upon
their integration in the genome (Table 4).
Class II non-LTR retroelements are
similar to beta retroviruses represented
by mammalian type B and D retroviruses
such as the mouse mammary tumor virus
(MMTV), Mason-PFzer monkey virus, and
primate lentiviruses. The latter include
human immunodeFciency virus (HIV). All
Class II retroelements are characterized
by 6-bp target site duplications (Table 5).
They were probably active in hominoids
including
Homo sapiens
.
Class III families represent the oldest
LTR retrotransposons detected in the hu-
man genome. Some of them were active
in the common ancestor of primates and
other mammals. Class III elements ampli-
Fed to a larger copy number than Class I
and Class II elements together. Class III
families are related to spumaviruses such
as human foamy virus, and they are char-
acterized by 5-bp target site duplications
(Table 6).
Structural features of LTR retrotransposons
A typical retrovirus is inserted into the
genome in the form of a provirus con-
taining two copies of 200 to 3000-bp long
LTRs, which are identical to each other
at the time of insertion (±ig. 8). Most
LTRs have conserved 5
0
-TG and CA-3
0
termini, but in some families such as
HERVK11 and HERVK11D, LTRs con-
tain TA-3
0
termini instead of CA-3
0
.The
internal portion of a provirus is deFned
as a sequence flanked by LTRs. Usually
Tab. 3
Classifcation oF human LTR retrotransposons.
Human LTR
retrotransposons
Percentage of
thegenome[%
]
Target site
duplications [bp]
Related exogenous
retroviruses
Age [Myr]
Class I
2.5
4–5
Gamma retroviruses (C type
a
):
Murine leukemia virus
20–80
Class II
0.5
6
Beta retroviruses (B type
b
,D
type
c
): mouse mammary
tumor virus; Mason–Pfzer
monkey virus; lentiviruses
1–35
Class III
6
5
Spumaviruses: human Foamy
virus
20–150
Distinctive Features seen in transmission electron micrographs:
a
Central and spherical viral core, ‘‘C particles’’.
b
Accentric and spherical viral core, ‘‘B particles’’.
c
Cylindrical core, ‘‘D particles’’.
