Biology Reference
In-Depth Information
Alu
repeats share a recognizable consensus sequence but the extent of homol-
ogy to this consensus varies from 72% to 99% (Kariya
et al
., 1987; Batzer
et al
.,
1990). Human
Alu
sequences are ~300 bp in length, are polyadenylated and con-
sist of two related sequences each between 120 and 150 bp long separated by an A-
rich region (
Figure 1.7
).
Alu
sequences appear to be degenerate forms of 7SL RNA
(
RN7SL
) that have been reverse transcribed and integrated into the genome (Ullu
and Tschudi, 1984). As to a possible function for
Alu
sequences, the question still
remains open (Schmid, 1998).
Several reports of transcription of
Alu
sequences either by RNA polymerase II
or III have appeared (Maraia
et al
., 1993) but their transcription is often silenced
by DNA methylation (Liu
et al
., 1994) and/or nucleosome positioning (Englander
et al
., 1993).
Alu
sequences contain an internal RNA polymerase III promoter
(Jelinek and Schmid 1982), a functional retinoic acid response element (Vansant
and Reynolds, 1995) and a regulatory element that can confer positive or negative
regulation of transcription upon a variety of promoters
in vitro
(Brini
et al
., 1993).
The presence of the polIII promoter is important since it ensures high expression
in the germline, a prerequisite for efficient transposition.
There are at least four different types of
Alu
sequence which belong to two dis-
tinct subfamilies (Jurka and Smith, 1988; Britten
et al
., 1988; Deininger and
Batzer, 1993). Some types of
Alu
sequence are human-specific (Batzer
et al
., 1990;
Batzer and Deininger, 1991) and these appear to be derived from a number of
different but closely related master copies or 'source genes' (Matera
et al
., 1990a).
The vast majority of human
Alu
sequences appear to be transcriptionally inert.
Some of the human-specific subfamilies are transpositionally competent and these
may also be transcriptionally active (Matera
et al
., 1990b; Sinnett
et al
., 1992).
Alu
repeats are concentrated in R bands in metaphase chromosomes (Korenberg
and Rykowski, 1988) whereas these repeats are under-represented in other regions
(e.g. centric heterochromatin) (Moyzis
et al
., 1989). R bands are G+C rich, replicate
their DNA early in S phase and condense late in mitotic prophase. R bands also
contain the bulk of active gene sequences. One consequence of the nonrandom
(A)
n
Alu
(A)
n
5'
3'
7SL RNA
100 bp
Figure 1.7.
Structure of the human
Alu
repeat element compared with the related 7SL
RNA. A 155 bp portion of the 7SL RNA is absent from the
Alu
sequence as indicated.
Poly(A) stretches are denoted by (A)
n
.