Chicken Genome
545
for the chicken. The high repeat content
(
50%) in mammalian genomes has been
a major problem with the WGS strategy;
however, in the chicken, the repeat content
is only 10 to 15%. This was shown dramati-
cally in the repeat plots of Fnished genome
sequences of human, mouse, and chicken.
Also, more than 75% of WGS sequences
from chicken BAC clones were contained
in a single contig compared to only 25% in
the mouse. The sequence will be based on
a female (the heterogametic sex in chicken)
inbred Jungle ±owl used to create the East
Lansing genetic linkage map.
6.2
Comparative Sequencing and Identifcation
oF Conserved Regions
The chicken has often been used as
an outgroup species in many evolution-
ary studies, in particular, in the study
of the evolution of genes and genomes.
Recently, there has been a rise in com-
parative genome analysis between long
sequences in mammals (mostly human
and mouse) and the chicken as a tool
to identify conserved regions with the
potential to function as regulatory se-
quences. This type of analysis began on
a smaller scale in earlier gene sequenc-
ing studies in which conserved sequence
motifs were found in both mammals and
chicken. ±or example, it was identiFed that
NF
κ
B, PEA1, PEA3
,and
C/EBP
transcrip-
tion factor binding sites are associated
with chicken inducible nitric-oxide syn-
thase. It was shown that transcription
binding sites in the 5
0
-flanking region of
the
TGFB3
gene are conserved in chick-
ens and humans. It was shown that the
lens-preferred alphaA-crystallin gene con-
tains a conserved stretch in the 5
0
-flanking
region of the chicken and mouse genes.
The 5
0
-half of this region has consensus
binding sites for
AP-1
and other tran-
scription factors. ±urthermore, the mouse
and chicken alphaA-crystallin genes are
expressed with lens speciFcity using a
similar assortment of transcription factors
but with a different physical arrangement
of their respective cis-elements within the
promoter region.
A detailed study of the
SCL
locus com-
pared 36 kb around the chicken locus with
orthologous regions in human and mouse.
In all the three species, the
SIL
and
MAP17
genes flanked the
SCL
gene. A detailed
analysis also conFrmed a number of pre-
viously characterized enhancer sequences
and predicted a new enhancer 23-kb down-
stream of the
SCL
promoter start site.
Another example is the comparison of the
alpha-globin
gene in a number of species
(human,mouse,chicken,and±ugu)span-
ning 400 million years of evolution. In this
study, several conserved motifs were iden-
tiFed in all the four species that suggested
a common conserved function. A recent
study on
SOX2
gene expression in the
chick identiFed Fve functional-enhancer
sequences in a 50-kb region flanking
the chicken gene, after electroporation of
embryos with various constructs. The ex-
citing Fnding was that these functionally
identiFed
SOX2
enhancers corresponded
exactly to the extragenic sequence blocks
conspicuously conserved between chicken
and mammals, but which were not de-
tected by sequence comparison among
mammals. These large-scale studies re-
quire new bioinformatic tools such as
PipMaker
. An example of the type of anal-
ysis is shown in ±ig. 5 in which a region
on human chromosome 19p13.1 (contig
NT
011295) is compared with orthologous
regions on chicken and mouse chromo-
somes. The exciting thing about this is that
the chick sequence is so well conserved
previous page 1219 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 1221 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off