Alu sequences and human evolution
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Thu Jul 21 04:30:05 EST 1994
Subj: ALU SEQUENCES and human evolution
Date: 94-07-20 07:48:40 EDT
From: haross at students.wisc.edu
MESSAGE OF 1 OF 2
Here is some info on Alu represents and human evolution. The second part
this message provides information on viral taxonomy.
Alu repeats result from RNA that has been reversely transcribed back into
the DNA. There are hundreds of thousands of sequences and they make up
5% of the total DNA. The full sequence is about 200 nucleotides long and
very closely resembles 7SL RNA. This RNA binds with 6 proteins to form the
signal recognition particle (SRP). When a new protein is being synthesized
the SRP binds the nascent protein chain, halting synthesis until the SRP
bind to an endoplasmic reticulum (ER) channel protein (Sec61p). This
the ribosome to bind to the ER and the nascent protein to translocate into
Whether the reverse transcriptase arose via mutation, viral infection or
some other means is not known.
Hope these shed some light.
ALU AND EVOLUTION
Shen MR. Batzer MA. Deininger PL.
Evolution of the master Alu gene(s).
Journal of Molecular Evolution. 33(4):311-20, 1991 Oct.
A comparison of Alu sequences that comprise more recently amplified Alu
subfamilies was made. There are 18 individual diagnostic mutations
associated with the different subfamilies. This analysis confirmed that
the formation of each subfamily can be explained by the sequential
accumulation of mutations relative to the previous subfamily. Polymerase
chain reaction amplification of orthologous loci in several primate
species allowed us to determine the time of insertion of Alu sequences
individual loci. These data suggest that the vast majority of Alu
amplified at any given time comprised a single Alu subfamily. We find
that, although the individual divergence relative to a consensus
correlate reasonably well with sequence age, the diagnostic mutations
a more accurate measure of the age of any individual Alu family member.
Our data are consistent with a model in which all Alu family members
been made from a single master gene or from a series of sequential
genes. This master gene(s) accumulated diagnostic base changes,
in the amplification of different subfamilies from the master gene at
different times in primate evolution. The changes in the master gene(s)
probably occurred individually, but their appearance is clearly
punctuated. Ten of them have occurred within an approximately
15-million-year time span, 40-25 million years ago, and 8 changes have
occurred within the last 5 million years. Surprisingly, no changes
appeared in the 20 million years separating these periods.
Gonzalez IL. Tugendreich S. Hieter P. Sylvester JE.
Fixation times of retroposons in the ribosomal DNA spacer of human and
Genomics. 18(1):29-36, 1993 Oct.
We have investigated the presence/absence of two types of retroposed
sequences found in human ribosomal DNA in equivalent positions in
chimpanzee, gorilla, orangutan, gibbon, and rhesus monkey rDNA. These
sequences are one pseudogene derived from the single-copy cdc27hs gene
seven complete Alu elements. The 2-kb pseudogene is present in the apes
but not in Old World monkeys, indicating fixation in an ape ancestor.
of the Alu elements are shared by the whole set of primates studied,
indicating insertion and fixation prior to the split of the ape and Old
World monkey lineages. One is absent only from the rhesus monkey rDNA,
another is absent from both gibbon and rhesus rDNA, indicating fixation
different times in primate evolutionary history. Since branching times
the primate phylogenetic tree are known from a combination of the fossil
record and multiple molecular data sets, it is possible to compare Alu
fixation times determined from the phylogenetic information with those
calculated from Alu element mutation rates.
Chang DY. Maraia RJ.
A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro.
Journal of Biological Chemistry. 268(9):6423-8, 1993 Mar 25.
B1 and Alu are sequence-homologous interspersed elements of unknown
function that have expanded in the genomes of mice and humans,
respectively. A minority of B1 and Alu sequences are expressed as small
cytoplasmic RNAs. These RNAs have conserved a secondary structure motif
also present in signal recognition particle (SRP) RNA despite
sequence divergence, whereas random B1 and Alu sequences have not. This
RNA structure has also been conserved by the source sequences that gave
rise to successive transpositions during B1 and Alu evolution. In the
present work small cytoplasmic B1 and Alu RNAs synthesized in vitro were
found to bind a cellular protein by mobility shift and UV cross-linking
analyses. The mouse and human proteins demonstrate the same specificity
a panel of competitor RNAs. Results using mutated B1 RNA indicate that a
single strand loop in the conserved Alu motif is essential for binding.
Previous work by Strub et al. (Stub, K., Moss, J. B., and Walter, P.
(1991) Mol. Cell. Biol. 11, 3949-3959) demonstrated that the
protein SRP 9/14 does not footprint to this region of SRP RNA. This
observation coupled with the failure of anti-SRP/9 antibodies to
SRP 9/14 in the B1 RNA-protein complex as well as the apparent mass and
other characteristics of the protein described here suggest that it is a
novel B1-Alu RNA-binding protein. Conservation of primary and secondary
structure by B1 and Alu small cytoplasmic RNAs as well as features of
their specific expression and ability to interact with the conserved
binding protein indicate that these RNAs are more homologous than
Hellmann-Blumberg U. Hintz MF. Gatewood JM. Schmid CW.
Department of Chemistry, University of California, Davis 95616.
Developmental differences in methylation of human Alu repeats.
Molecular & Cellular Biology. 13(8):4523-30, 1993 Aug.
Alu repeats are especially rich in CpG dinucleotides, the principal
sites for DNA methylation in eukaryotes. The methylation state of Alus
different human tissues is investigated by simple, direct genomic blot
analysis exploiting recent theoretical and practical advances concerning
Alu sequence evolution. Whereas Alus are almost completely methylated in
somatic tissues such as spleen, they are hypomethylated in the male germ
line and tissues which depend on the differential expression of the
paternal genome complement for development. In particular, we have
identified a subset enriched in young Alus whose CpGs appear to be
completely unmethylated in sperm DNA. The existence of this subset
potentially explains the conservation of CpG dinucleotides in active Alu
source genes. These profound, sequence-specific developmental changes in
the methylation state of Alu repeats suggest a function for Alu
at the DNA level, such as a role in genomic imprinting.
Minghetti PP. Dugaiczyk A.
The emergence of new DNA repeats and the divergence of primates.
Proceedings of the National Academy of Sciences of the United States of
America. 90(5):1872-6, 1993 Mar 1.
We have identified four genetic novelties that are fixed in specific
primate lineages and hence can serve as phylogenetic time markers. One
DNA repeat is present in the human lineage but is absent from the great
apes. Another Alu DNA repeat is present in the gorilla lineage but is
absent from the human, chimpanzee, and orangutan. A progenitor Xba1
element is present in the human, chimpanzee, gorilla, and orangutan, but
only in the human lineage did it give rise to a transposed progeny,
The saltatory appearance of Xba2 is an example of a one-time event in
evolutionary history of a species. The enolase pseudogene, known to be
present as a single copy in the human, was found to be present in four
other primates, including the baboon, an Old World monkey. Using the
accepted value of 5 x 10(-9) nucleotide substitutions per site per year
the evolutionary rate for pseudogenes, we calculated that the enolase
pseudogene arose approximately 14 million years ago. The calculated age
for this pseudogene and its presence in the baboon are incongruent with
each other, since Old World monkeys are considered to have diverged from
the hominid lineage some 30 million years ago. Thus the rate of
in the enolase pseudogene is only about 2.5 x 10(-9) substitutions per
site per year, or half the rate in other pseudogenes. It is concluded
rates of substitution vary between species, even for similar DNA
such as pseudogenes. We submit that new DNA repeats arise in the genomes
of species in irreversible and punctuated events and hence can be used
molecular time markers to decipher phylogenies.
Theoretical Biology and Biophysics Group, Los Alamos National
Origin of the Alu family: a family of Alu-like monomers gave birth to
left and the right arms of the Alu elements.
Nucleic Acids Research. 20(13):3397-401, 1992 Jul 11.
The Alu dimeric elements are a common feature of the primate genomes,
where they constitute a family of related sequences (1). The
identification of a free left Alu monomer (FLAM) family plus a free
Alu monomer (FRAM) family suggests that the dimeric structure results
the fusion of a FLAM sequence with a FRAM sequence (2). Here, we
a very old Alu-like monomeric family, referred to as FAM for fossil Alu
monomer. This family arose from a 7SL RNA sequence and gave birth to the
FLAM and FRAM families. From the results obtained, the evolution of the
Alu family can be subdivided into two phases. The first phase, which
involves only monomeric elements, is characterized by deep remodelling
the progenitor sequences and ends with the appearance of the first Alu
dimeric element through the fusion of a FLAM and a FRAM element. The
second phase, still in progress, starts with the first Alu dimeric
element. This phase is characterized by the stabilization of the
Liu WM. Leeflang EP. Schmid CW.
Unusual sequences of two old, inactive human Alu repeats.
Biochimica et Biophysica Acta. 1132(3):306-8, 1992 Oct 20.
Two human Alu repeats terminating in an oligo(T) run rather than the
A-rich 3' tail were isolated by library screening. Base sequence
comparisons reveal that these unusual Alus are also exceptionally
divergent from other Alu family members implying that they are
evolutionarily old. Unlike other members of the family, they are not
transcribed in vitro by RNA polymerase III (Pol III) suggesting a
explanation for how Alu source genes might become inactive with age.
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