nervous and muscular system of the embryo and
regulates the thoracic and abdominal development.
Caudal (cad) is another patterning gene that is
responsible for anterior/posterior determination of the
embryo. Bicoid (bcd) is the transcription factor that
binds to the promoter of hunchback (hb), a patterning
gene expressed at head and tail of the embryo. Dorsal
(dl) is another patterning gene that has an expression
gradient that decreases as going from the ventral side
to the dorsal side. Which means dorsal expression is
highest at the mesoderm of the embryo’s ventral part
and close to zero at the embryo’s dorsal side.
Zerknullt (zen) expression can be inhibited by any
level of dorsal gene product, that’s why it’s a
patterning gene which can only be found at the dorsal
part of the embryo. CG1641/sisA is an ubiquitous
Class 1 gene whose expression is theoretically evenly
distributed through the whole embryo. However, it is
regulated by so many patterning genes that are
expressed at different parts of the embryo. This
further demonstrated that sisA can be found at
anywhere of the embryo. What’s more important is
that due to the regulation of so many patterning
transcription factors (Kr, cad, bcd, dl, zen), sisA
expression level is uneven across the whole embryo.
Therefore, Class 1 genes’ expression should be
everywhere in the embryo if the Zelda is functional
but the expression levels are diverse at different area
caused by the regulation of patterning gene products.
The JASPER result of the patterning gene,
CG2411/ptc, shown in Figure 4. and Table 3.4., also
indicates high level of Zelda binding. However, in
this case, Zelda binds to the enhancer of the gene to
increase the expression level instead of completely
controlling the switch on/off of the transcription.
Around the 8656150bp Zelda binding peak shown by
Figure 4a, there is also very high level binding of
Trithorax-like gene (Trl) (Table 3). The Trl gene
product is a transcription factor for chromatin
modification. Trl has even higher binding score to ptc
than Zelda. According to the expression patterning
shown in Figure 5, Trl is an ubiquitous Class 1 gene.
However the transcription factor with the highest
binding score here is Dorsal switch protein 1 (Dsp1)
according to Table 3. This transcription factor prefer
to bind a single strand of DNA molecules and
subsequently unwind the double-stranded DNA. It is
an ubiquitous gene according to the BDGP data
shown in Figure 5. It makes sense as all genes in the
embryo can only be transcribed after the double-
stranded DNA is unwound. CG2411/ptc has
patterning expression through the whole embryo, but
it is regulated by high level of ubiquitous gene
products such as Trl and Dsp1 situated at its enhancer
region. This demonstrated that Class 2 genes’
expression is also controlled by many Class 1 genes.
The reason might be that Class 1 genes have generic
functions required for transcription of all genes, the
unwinding function of Dsp1 is an example.
Therefore, no matter the gene’s expression is
patterning or ubiquitous, its transcription is regulated
by many ubiquitous Class 1 genes. The second Zelda
binding peak on CG2411/ptc is at 8657916bp and
shown by Figure 4b. In the 400bp region around this
peak, zen, bcd, and dl are also found at high level
according to Table 4. These three patterning genes
are mentioned above. Another transcription factor
found at high score is snail (sna), a patterning gene
that is essential for mesoderm development. Sna is
activated by high level dl and is expressed in
mesoderm at the ventral side of the embryo shown in
Figure 5. Sna is also found at high level around the
8656150bp Zelda binding peak represented by
Figure 4a. Although there’s no data of ptc’s
expression pattern in BDGP, we can estimate its
pattern according to the patterns of the patterning
gene which regulate its transcription. dl and sna are
expressed at mesoderm. Bicoid (bcd) is quite
important for head development and is expressed at
highest concentration in head. zen can only be found
at dorsal side of the embryo because of the inhibition
by dl. Therefore, we can estimate that ptc is expressed
mainly at the head, ventral and dorsal part of the
embryo.
5 CONCLUSIONS
In conclusion, graphs from IGB are reliable tools to
determine whether a Drosophila gene is Class 1
(ubiquitous) or Class 2 (patterning). According to
JASPAR data of the Class 1 CG1641/sisA and Class
2 CG2411/ptc, Class 1 gene is totally controlled by
Zelda that switch it on or off by directly binding to
the promoter. However, Zelda is not the only factor
controlling the Class 1 gene transcription. On the one
hand, there are many patterning gene transcription
factors that regulate the transcription level of the
Class 1 gene. That’s why the theoretically ubiquitous
expression level of Class 1 gene is actually uneven
across the embryo. On the other hand, Class 2 genes
are also regulated by ubiquitous Class 1 gene
products because some functions of these
ubiquitously expressed products can influence the
transcription rates of all genes in the organism. This
research, underpinned by powerful software and
pioneering databases, revealed the complexity of
genes’ network during early development of animals.