Promoters and transcription factors - Human Gene Evolution - page 222

5.1.1 Evolutionary conservation of cis-acting elements and 'phylogenetic
footprinting'

Sequence conservation in promoter regions is usually held to be an indicator of
functional importance and may therefore be used as a rough guide to the location
of cis -acting regulatory elements that might bind trans -acting factors. Such phylo-
genetic footprinting has proven successful in locating trans -acting factor binding
sites in a considerable number of human genes including the

-globin ( HBE1 ;

11p15.5) gene (Gumucio et al ., 1993; Hardison et al ., 1997), the 1-globin ( HBG1 ;

11p15.5) gene (Tagle et al ., 1988), the -globin ( HBB ; 11p15.5) gene locus control

region (Shelton et al ., 1997), the cytochrome c oxidase subunit Vb ( COX5B ; 2cen-
q13) gene (Bachman et al ., 1996), the Duchenne muscular dystrophy ( DMD ;
Xp21) gene (Fracasso and Patarnello 1998), the hormone-sensitive lipase ( LIPE ;
19q13) gene (Talmud et al ., 1998) and the cystic fibrosis transmembrane conduc-
tance regulator ( CFTR ; 7q31.3) gene (Vuillaumier et al ., 1997) among others. It
was also instrumental in identifying the CArG sequence motif [CC(A/T rich) 6 GG]
important for the regulation of the cardiac

-actin ( ACTC ; 15q14) gene (Taylor

et al ., 1988).
Phylogenetic footprinting has been used to identify regulatory elements in the
promoter regions of the rapidly evolving SRY (Yp11.3) genes of 10 mammalian
species (Margarit et al ., 1998). A total of 10 putative regulatory elements were
identified by these means ( Figure 5.1 ). Interestingly, differences were apparent
between the SRY promoters not only in terms of the presence/absence of specific
motifs and motif copy number, but also in the spacing between motifs, their rela-
tive location and orientation (sense or antisense strand). Conserved elements in
the SRY gene promoters within each taxonomic group (primates, bovids, rodents)
did however tend to occupy orthologous positions.
The study of Vuillaumier et al . (1997) identified eleven DNase I-hypersensitive
phylogenetic footprints in a 3.5 kb region of the CFTR gene (7q31.3) promoter
when eight mammals from four different orders were compared. Two of these
footprints, which corresponded to the cAMP response element and the PMA-
responsive element, were conserved in all species examined, a finding which
probably reflects the vital importance of transcriptional control through the
cAMP and diacylglyerol pathways respectively. By contrast, a 300 bp
purine.pyrimidine stretch, thought to represent a negative element of basal tran-
scription, was found to be present only in the Cftr genes of rodents. Studies of the
globin genes have also shown that some motifs may be of functional importance
in one species but not be conserved between species, for example two Sp1-binding
sites in the human HBB gene locus control region (Shelton et al ., 1997). Such
inter-specific differences are explored further in Section 5.1.4.
A variation on this theme is differential phylogenetic footprinting which utilizes
the promoter sequences of two extant species representing the most closely
related lineages between which a difference in developmental expression pattern
can be detected. An example of its successful use was in the study of the galago
and human -globin ( HBG1 ) gene promoters (Gumucio et al ., 1994; Section

5.1.8). Differential phylogenetic footprinting has also been used to study the pro-
moters of the apolipoprotein AI ( APOA1 ; 11q23.3) genes of human and African
green monkey in order to assess the functional significance of species-specific