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Alu-Mediated Phylogenetic Novelties in Gene Regulation and Development
Alu-Mediated Phylogenetic Novelties in Gene Regulation and Development
Department of Biochemistry Differential gene expression lies at the heart of biology and is responsible
University of California for all developmental processes, including the growth and differentiation
Riverside, CA 92521, USA of cells. Perhaps even speciation could be de®ned as a change in differen-
tial gene expression over evolutionary time. The present work is a phylo-
genetic study of four Alu elements known to have gene regulatory
functions in the human. The four elements have been shown to regulate
the parathyroid hormone (PTH) gene via a negative calcium-response
element, the hematopoietic cell-speci®c FceRI-g receptor gene via a cis-act-
ing positive/negative regulatory element, the CNS-speci®c nicotinic
acetylcholine receptor a3 gene via a cis-acting positive/negative control
element, and the T-cell-speci®c CD8a gene via a complex transcriptional
regulator. The four Alu elements that impact differential gene expression
were found to be differentially distributed among seven primate species
(human, chimpanzee, gorilla, orangutan, baboon, rhesus, and macaque)
in a way that is congruent with an accepted phylogeny of these species.
The results establish a link between gene regulation and the divergence
of primates. This evolutionary variation in gene regulation also suggests
a novel experimental system to study the very complex transcriptional
regulation of gene expression, by studying side-by-side the regulation of
the same gene from two primate species that differ in the cis-acting regu-
latory elements of the gene.
# 2000 Academic Press
Keywords: Alu sequences; factor-binding sites; gene regulation; saltatory
*Corresponding author events
Calcium regulation of the parathyroid hormone Structural and functional features of the
(PTH) gene nicotinic acetylcholine receptor a 3 gene
A negative calcium-response element type 2 Nicotinic acetylcholine receptors are ligand-
(nCARE) is a 15 bp sequence with a 12 bp palin- gated ion channels expressed at the neuromuscular
dromic core which was identi®ed approximately junction and in several areas of the vertebrate cen-
3.6 kb upstream from the transcription site of the tral nervous system. Different structural subunits
human parathyroid hormone (PTH) gene (Okazaki combine to form different receptor subtypes with
et al., 1991). The nCARE2, along with a distinct, distinctive pharmacological and electrophysiologi-
more downstream situated nCARE element are cal properties, and the fast excitatory postsynaptic
Phylogenetic Novelties 933
potential is due to the activation of nicotinic acetyl- chain of the IgE receptor gene, new transcription
choline receptors that contain a3 as the essential control elements of the nicotinic receptor gene
agonist-binding subunit (McGehee & Role, 1995). arose in the lineage leading to higher primates.
The expression of certain subunits can be restricted
to very few brain structures (Wada et al., 1989; Zoli T-cell specific transcriptional enhancer in the
et al., 1995), implying that stringent controls must CD8aa gene
be exerted to achieve such ®ne tuning of spatial
and developmental regulation. The a3 promoter Expressed on the surface of T-cells, CD8 interacts
was found to be under the control of upstream extracellularly with the major histocompatibility
sequences that reside with an Alu and contain both complex (MHC) molecules (Norment et al., 1988)
and intracellularly associates with the tyrosine
a positive and a negative control element
kinase p56lck (Chalupny et al., 1991). Expression of
(Fornasari et al., 1997). A diagram of the 50 -region
the human CD8a gene is restricted to cells of the
of this gene is shown in Figure 3(a). lymphoid lineage and it is developmentally regu-
Using primers ¯anking the upstream Alu con- lated during thymopoiesis (Leiden, 1992). In the
taining the cis-acting regulatory elements, we last (5th) intron of this gene, a T-cell-speci®c
ampli®ed the orthologous regions from seven pri- enhancer was identi®ed that is partially located in
mate species and veri®ed the identity of the PCR an Alu element (Hambor et al., 1993). This CD8a
products by DNA sequencing of their entire length, intronic enhancer is a complex transcriptional regu-
although only critical regions are shown lator containing seven binding sites for six tran-
(Figure 3(b) and (c)). This regulatory Alu element is scription factors: GATA-3, LyF-1 (two sites),
present in humans and great apes, but absent from bHLH, TCF-1, CRE, and Ets-1. Four of these bind-
Old World monkey species, where only the empty ing sites reside in the Alu element. There is actually
target site is present. Similar to the results on the g a full-length and a half-Alu repeat in close proxi-
934 Phylogenetic Novelties
Figure 2. Analysis of primate genomic DNA for the presence or absence of an orthologous Alu repeat carrying a
positive and negative control element of transcription. (a) A diagram of the 50 -¯anking region upstream of the human
high-af®nity IgE receptor (FceRI-g) gene (reconstructed from Brini et al., 1993), showing the position of the Alu repeat
carrying a positive and negative control element. (b) PCR analysis of the orthologous Alu locus in the primates. The
following primers were used: Fc Pr-1, 50 -TTCAATGACCAACTCCTAACCCAC; Fc Pr-2, 50 -TGCCCACATAACTTGG-
TAAACCAC. Samples (10 ml) of PCR mixtures (see Materials and Methods) were electrophoresed in a 5 % polyacryl-
amide gel. Molecular mass standards (Std) are indicated in base-pairs (bp), the remaining lanes contain PCR products
from the various primate species. DNA bands in the 500 bp region indicate the presence of the Alu repeat, those in
the 200 bp regions, its absence. Small differences in mobility of the PCR bands between the various primates are
caused primarily by variable lengths of the poly(A) strech terminating each Alu, and by small insertions/deletions in
the ¯anking regions. (c) DNA sequence of regions surrounding and including the orthologous FceRI-g Alu repeat, or
its unoccupied target site. Nucleotides identical with the top sequence (ÿ), deletions (), and target sites and terminal
repeats (underlined) are indicated.
mity and in an opposite (tail-to-tail) orientation. deposited in GenBank under accession numbers
A map of this region is shown in Figure 4(a). AF251315; AF251316; AF251317; AF251318;
Using ¯anking primers, we ampli®ed by PCR AF251319; AF251320. The corresponding human
the one and a half-Alu structure, including ¯anking sequence has been deposited under M27161 by
regions, and sequenced it from the seven primate Nakayama et al. (1989).
species (Figure 4(b) and (c)). The full-size Alu, con-
taining the four transcription factor binding sites, Discussion
is found only in humans and great apes, while the
50 adjacent half-Alu is present in higher primates The de®ning event of speciation is a transition
and Old World monkeys (Figure 5). The present from being to becoming, but the underlying geno-
sequence from the non-human primates has been mic event(s) of such a transition elude identi®-
Phylogenetic Novelties 935
Figure 3. Analysis of primate genomic DNA for the presence or absence of an orthologous Alu repeat carrying a
positive and negative control element of transcription. (a) A diagram of the 50 -¯anking region upstream of the human
a3 nicotinic receptor subunit gene (reconstructed from Fornasari et al., 1997), showing the position of the Alu repeat
carrying a positive and negative control element. (b) PCR analysis of the orthologous Alu locus in the primates. The
following primers were used: a3 Pr-1, 50 -GGTACCATCATCCTGCCTCGACAAT; a3 Pr-2, 50 -CGCCGTAGGAGA-
GACGCTAACACA. Samples (10 ml) of PCR mixtures (see Materials and Methods) were electrophoresed in a 5 %
polyacrylamide gel. Molecular mass standards (Std) are indicated in base-pairs (bp), the remaining lanes contain PCR
products from the various primate species. DNA bands in the 500 bp region indicate the presence of the Alu repeat,
those in the 200 bp regions, its absence. Small differences in mobility of the PCR products between the various pri-
mates are caused by variable lengths of the poly(A) strech terminating each Alu, and by small insertions/deletions in
the ¯anking regions. (c) DNA sequence of regions surrounding and including the orthologous a3 Alu repeat, or its
unoccupied target site. Nucleotides identical with the top sequence (ÿ), target sites and terminal repeats (underlined)
are indicated.
cation. Perhaps the recruitment of cis-regulatory Alu insertion and primate evolution; a correlation
elements, which causes the transcription of genes with a mechanism of speciation remains to be
in different spatial or developmental contexts, established. Although the differential distribution
could belong to this category of events. We have of the presently identi®ed Alus is not depicted on a
recently shown that a differential distribution of phylogenetic tree, it is important to note that it is
Alu DNA elements in primates can be used to not a haphazard distribution. The four Alus carry-
reconstruct an unambiguous tree of primate phylo- ing gene regulatory elements are distributed
geny (Hamdi et al., 1999). In the present study, we among seven primate species in a way that is con-
provide examples of differential distribution of gruent with an accepted phylogeny of human and
Alu-embedded gene regulatory elements in pri- apes, and the Old World monkey species. How
mate species that establish a correlation between these genes are actually regulated in the non-
936 Phylogenetic Novelties
human species, and how a differential regulation it is found in contemporary New World monkeys,
might contribute to the mechanism of speciation, which were not included in our present work.
must await additional studies.
Genetic novelties at the roots of
Control element shared by great apes and Old higher primates
World monkeys
The Alu elements residing upstream of the
The Alu element residing upstream of the PTH human FceRI-g gene (Figure 2), upstream of the
gene and controlling PTH expression in the nicotinic a3 gene promoter (Figure 3), and within
human, was found to be present in all the primate the CD8a gene (Figures 4 and 5) are differentially
species studied (Figure 1). This is an example of an distributed in primate species. They are present in
old insertion and retention of function from a time higher primates, but absent from the Old World
deep in the past in primate evolution. The phyloge- monkeys, where only an empty target site is pre-
netic origin of this PTH Alu could be even older, if sent at the orthologous site, and no Alu transposi-
Phylogenetic Novelties 937
Figure 5. Nucleotide sequence of the CD8a intronic enhancer in the various primates (H, human; C, chimpanzee;
G, gorilla; O, orangutan; B, baboon; R, rhesus; M, lion-tailed macaque). The T in position 1 corresponds to position 4
in CD8a Pr-1 (see Figure 4); and the position of CD8a Pr-2 is 63 to 95 nucleotides downstream of the last T in pos-
ition 600. Nucleotides identical with the top (human) sequence (ÿ); deletions (), the target sites, terminal repeats,
and the cis-regulatory elements (underlined) and the beginning of the half-Alu and the full-size Alu (arrows) are
indicated. The two Alu repeats are in a tail-to-tail orientation, separated by a short stretch of G bases, and they are
terminated by a stretch of poly(A) of different length in the various primates. These and additional sequences have
been deposited in GenBank under accession numbers AF251315, AF251316, AF251317, AF251318, AF251319 and
AF251320.
938 Phylogenetic Novelties
tion took place. These elements represent a gain of must be only a matter of time before human-
function in the higher primates, considering that speci®c Alus are found to control gene expression.
the ancestral state of an Alu character is always its
absence (Hamdi et al., 1999). If the newly arisen
Alus operate in cell-speci®c and developmental Materials and Methods
gene regulation in higher primates, as they do in
DNA
humans, then the gain of these regulations was
attained at the roots to higher primates and was Peripheral blood (5 ml) was collected into 10 mM
carried over to all descendent lineages. EDTA and used to isolate white blood cells according to
The CD8a example provides more speci®c the method of Kan et al. (1997). Genomic DNA was iso-
details about species-speci®c differences in gene lated from the white blood cells using the Qiagen
regulatory elements. In humans, the Alu insertion QIAamp kit and the manufacturer's protocol. DNA from
contributed to the evolution of a complex tran- the following species was used: human (Homo sapiens),
chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla),
scriptional regulatory element: four binding sites
orangutan (Pongo pygmaeus), baboon (Papio cynocephalus
for transcription factors are within it, and they anubis), rhesus monkey (Macaca mulatta), and lion-tailed
have been shown to participate in cell-speci®c gene macaque (Macaca silenus). Human blood was obtained
regulation (Hambor et al., 1993). This regulatory from a local blood bank while primate genomic DNA or
Alu is present in the higher primates (Figure 4), blood samples were obtained from: Loma Linda Univer-
and its four regulatory elements are largely con- sity, CA; San Diego ZOO/CRES; University of California
served in the four primate species (Figure 5). Davis Primate Research Center; University of Pittsburgh
GATA-3 has two point mutation differences Medical Center; The Upjohn Company; Yerkes Primate
between human and the other primates, and may Research Center.
or may not function in the same way in the four
primate species (some differences are allowed PCR
within a concensus sequence in cis-regulatory
elements). The sequences of the remaining three Ingredients for the PCR reaction (30 ml) included:
(bHLH and two sites of LyF-1) are identical in 20 mM Tris-HCl (pH 8.3), 50 mM KCl, 2.5 mM MgCl2,
human, chimp, and gorilla, and differ only by one 250 mM each dNTP, 0.2 mM each primer (described in
the Figure legends), 0.3 mg of genomic DNA, and 0.9
or two nucleotides in the orangutan (Figure 5). It
unit of Taq polymerase. Reactions were performed in a
seems safe to postulate that the four regulatory Stratagene Robocycler under the following conditions:
elements were ``active on arrival'' at the time of 96 C for two minutes, followed by 30 cycles of denatura-
the Alu transposition, rather than slowly aquired tion (96 C for 30 seconds), annealing (50 C-68 C for 30
their function by point mutations after the Alu seconds) and elongation (62 C-68 C for 30 seconds). The
transposition. This would represent a saltatory optimal annealing temperature for each set of primers
event at the roots to higher primates, with its con- was determined experimentally by ®rst running PCR
sequences carried over to descendent lineages. reactions on a temperature gradient ranging from 50 to
This regulatory Alu is absent from Old World 68 C. The last cycle was followed by a ®nal elongation
monkeys, but in its place there is an older half-Alu step (65 C for ®ve minutes). The reactions were stopped
by the addition of 3 ml of 0.25 M EDTA at 0 C, and ali-
in the structure of the CD8a gene. Could this half- quots were electrophoresed on a 5 % (w/v) polyacryl-
Alu provide the same transcriptional control amide (acrylamide to bis-acrylamide, 40:1, w/w) gel.
elements for the monkeys? In humans, where this
half-Alu is also present, although some 300 bp
further upstream within the intronic enhancer, no Sequencing of PCR-amplified DNA
binding sites for transcription factors were found Gel-puri®ed PCR products were either subcloned
experimentally by Hambor et al. (1993). Presently, or sequenced directly by the Maxam & Gilbert (1980) or
we sequenced this half-Alu from the seven primate the ABI dye-deoxy chain terminator cycle sequencing
species (Figure 5), and an inspection of this methodology.
sequence reveals no similarity to any of the bind-
ing sites identi®ed by Hambor et al. (1993) in the
full-size Alu of the human CD8a gene. It seems
safe to infer that the regulation of this gene must
be different in the monkey species. Further exper- Acknowledgments
iments will be required to show the transcriptional We thank Lars Dugaiczyk and Michael Capriotti for
differences in the non-human primates. These are computer graphics and photography of the Figures. This
complex experiments, considering that a large work was supported by grant CA-R-BCH-5820-H from
number of cis and trans-acting factors coordinate the University of California.
the process of gene transcription.
Considering that Alu elements can be speci®c to
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Edited by J. Karn
(Received 31 January 2000; received in revised form 13 April 2000; accepted 21 April 2000)