Biology Reference
In-Depth Information
Fruit fly
(
Drosophila melanogaster
)
Abd-B
abd-A
Ubx
~ 10 mb
Antp
Scr
Dfd
pb
lab
50 kb
Amphioxus
(
Branchiostoma floridae
)
Hox15
Hox14
Hox13
Hox11
Hox10
Hox9
Hox7
Hox6
Hox4
Hox3
50 kb
Mouse
(
Mus musculus
)
Hoxa13
Hoxa9
Hoxa4
Hoxa1
Hoxb13
Hoxb9
Hoxb4
Hoxb1
Hoxc13
Hoxc9
Hoxc4
Hoxd13
Hoxd9
Hoxd4
Hoxd1
50 kb
Figure 4.3 Genomic organization of Hox clusters in Drosophila, Amphioxus, and mouse.
Hox genes are depicted as black boxes and other genes (transcripts) are shown as grey
boxes. Scale bars for each species are indicated below the clusters. Due to the incom-
plete annotation of the Amphioxus genome, no information is available for other tran-
scripts in the Hox cluster.
cluster is usually larger and may contain some repeats. Finally, in
Drosophila
species,
Hox
genes are even less strictly organized. Depending on the species,
the genes are found in two to three sub-clusters, with several possible inter-
nal breakpoints (
Fig. 4.2
;
Negre et al., 2003; Ranz et al., 1997
). In
D. mela-
nogaster
, the ANT-C cluster contains from the
lab
to the
Antp
genes, whereas
the BX-C cluster contains from
Ubx
to
Abd-B
. In other
Drosophila
species,
though,
Ubx
can be linked to ANT-C. Besides the split of the ancestral clus-
ter, the organization of both the semi-clusters and the
Hox
genes themselves
appear less structured.
Drosophila Hox
genes are spread out over larger
genomic regions, they may be transcribed in either orientations and they
may contain large introns (
Fig 4.3
). Yet,
Drosophila
spatial collinearity is
maintained, in spite of this highly derived organization. As such, regulation
of collinearity in
Drosophila
requires less of a cluster-wide type of regulation,
when compared to Amphioxus or mouse. This situation is even more strik-
ing in the tunicate Oikopleura, where
Hox
genes are completely isolated
from one another, yet they still keep some traces of collinear regulation
(
Seo et al., 2004
; see
Section 4.3
).
Drosophila
and mouse
Hox
gene activities differ further in their distribu-
tion along the AP axis (
Fig. 4.1
).
Drosophila Hox
genes are generally
expressed in non-overlapping domains, with the exception of the partially
overlapping
Ubx
and
abd-A
transcript territories (
Kosman et al., 2004
). In
contrast, the transcription of murine
Hox
genes is usually maintained along
the AP axis, such that the spatial distribution of the expression domains
