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’’.
previous page 270 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 272 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off