The Effect of the Transcription Factors Zelda, Dorsal, and Bicoid on
the Pattern Formation of Drosophile Melanogaster during the Early
Yibo Yang
XiWai international school, shanghai, 1100 Wenxiang Rd, China
Keywords: Fruit Fly, Zelda, Transcription Factors.
Abstract: The insect Drosophila melanogaster refers to the common species fruit fly. Many researches have been done
extensively on its marvelous early embryonic development, particularly during nuclear cycle 1-14, to better
understand the transcriptional mechanism behind it. Three well-acknowledged transcription factors have been
discovered by many scientists more than a decade ago, and they suggested that these transcription factors,
along with some others, are of vital importance to the decision making upon how a gene is expressed and
where it is expressed. In this study, I did some online researches, together with some reliable tools, to examine
the role of these transcription factors in regulating the gene expression and pattern formation of fruit fly. I
found out that, not surprisingly, these transcription factors have a profound and decisive impact on the
During the early development of Drosophila, the gene
expression of the embryo is dominated completely by
the mother. The mother decides which gene to be
expressed and puts those maternally-expressed gene
products into the embryo and allows the zygotic gene
expression to happen. The zygote then starts to
express some of the genes at about one hour of
development, and a lot of the genes that are expressed
turn out to be ubiquitous. Then at about three hours
of development, the egg is filled with those
ubiquitous genes that are expressed just about
everywhere. But sooner after this stage, the egg starts
to have what we call the patterning genes, because
they are expressed in certain patterns.
In this review, I focused on the effect of zelda,
dorsal, and bicoid, which are the three most important
transcription factors, on the early embryonic
development of Drosophila, in particular their
regulations on a single gene, and multiple genes that
give rise to specified pattern formations.
1.1 Overview of the
Maternal-To-Zygotic Passway,
The fertilized egg of Drosophila starts its development
very differently from you and me. Instead of cell
division, the egg starts with rapid division of nucleus.
When the number of nucleus in the embryo is large
enough, they migrate to the surface of the egg and start
the formation of cellular blastoderm, where the
plasma membrane starts to grow inward and
encapsulates those nucleus to form cells. In the earliest
stages of development, the zygotic genome is
generally inactive, with the embryo’s molecular
processes driven by proteins, RNAs and other
substances packed into the egg by the mother (Eisen,
2011). Later on, the embryo passes through a stage
during which developmental control is handed from
maternally provided gene products to those
synthesized from the zygotic genome, known as MZT
(Liang, Nien, [...], and Rushlow 2008). This complex
yet fascinating process has been studied extensively
by many scientists and college professors. Christine
Rushlow (Alberts, Johnson, Lewis at al. 2002), a
professor at NYU, together with some other scientists,
discovered that many of the early genes in Drosophila
share a cis-regulatory heptamer motifs, CAGGTAG
Yang, Y.
The Effect of the Transcription Factors Zelda, Dorsal, and Bicoid on the Pattern Formation of Drosophile Melanogaster during the Early Development.
DOI: 10.5220/0011251300003443
In Proceedings of the 4th International Conference on Biomedical Engineering and Bioinformatics (ICBEB 2022), pages 646-650
ISBN: 978-989-758-595-1
2022 by SCITEPRESS Science and Technology Publications, Lda. All rights reserved
and related sequences, collectively referred to as
TAGteam sites raised the possibility that dedicated
transcription factor could interact with these sites to
activate transcription. The protein that binds to the site
is known as Zelda (the zinc-finger protein). Rushlow
(Alberts, Johnson, Lewis at al. 2002) and her
colleagues suggested that Zelda has an important role
in the activation of the early zygotic genome and may
also be responsible for regulating maternal RNA
degradation during MZT.
Although the process of maternal regulation seems
to be short, it is crucial because it puts the necessary
gene products to the zygote, such as zelda, bicoid, and
dorsal, allowing for the zygotic gene expression and
specified pattern formation. Unlike zygotic mutation,
the mutation of maternally-expressed genes could be
fatal to the embryo. The mutant of maternally-
expressed gene bicoid, for example, will result in a
headless larva (Carrell, O'Connell, Jacobsen,
Pomeroy, Hayes, Reeves 2017). Table 1 and 2 shows
the two types of mutation.
Table 1: Maternal mutation Maternally required genes.
Parents Offspring
M/+♂ × M/+♀ M/M, M/+,+/+
all normal
M/M♂ M/M, M/+
all normal
+/+, M/+ or M/M ♂ × M/M♀ M/+, M/M
all mutant phenotype
Table 2: Zygotical mutation Zygotically required genes.
Parents Offspring
M/+♂ × M/+ M/+, +/+
More recent studies aimed at the interaction between
Zelda as well as other important transcription factors
in the formation of specified patterns during the early
embryonic development, particularly with some of
the maternally-expressed genes, such as bicoid and
dorsal. Those genes that are expressed in patterns are
collectively referred to as patterning genes. It is the
fly Drosophila melanogaster, more than any other
organism, that has transformed our understanding of
how genes govern the patterning of the body. The
anatomy of Drosophila is more complex than that of
C. elegans, with more than 100 times as many cells,
and it shows more obvious parallels with our own
body structure (Rushlow, Colosimo, Kirov 2001).
Therefore, to understand Drosophila is to initiate our
deep knowledge towards gene regulation, and dig
into its secret ever more.
According to the 2008 paper by Christine
Rushlow et al. (Zehra, Thomas 2016), the major burst
of activity occurs during 2 to 3h of development when
the embryo is undergoing cellular blastoderm
formation. Many genes contain TAGteam in their
upstream regulatory region including direct targets of
bicoid and dorsal. Christine Rushlow et al. (Zehra,
Kornberg 2016) performed a yeast one-hybrid screen
and gel shift on zen, a gene that requires TAGteam
for the early formation. What they found out was the
site CAGGTAG, which had the strongest affinity for
zelda. They then generated deletion alleles of zelda
by imprecise excision on gene CG12701(the gene
that translates zelda protein), and found abnormal
body formation in the embryo. Through a IGB test, I
then examined the Zelda binding peaks at the
promoter and enhancer sites of zen during nuclear
cycle 8 of embryo, and RNA polymerase binding
peaks on the gene during both nuclear cycle 13 wild
type and zelda knock-down. As shown in figure 1,
there is a high peak of zelda binding right at the start
of transcription, and several base pairs away at the
enhancer region. The blue lines below represent the
TAGteam, CAGGTAG. During NC13 WT, there are
several peaks of RNA polymerase binding peaks,
suggesting the proceeding of transcription. Whereas
during zkd13, all the peaks are gone. This result
further indicates the importance of zelda and
corresponds with the study by Christine Rushlow et
al. (Zehra, Thomas 2016).
The Effect of the Transcription Factors Zelda, Dorsal, and Bicoid on the Pattern Formation of Drosophile Melanogaster during the Early
Figure 1: The IGB analysis on zen.
Figure 2: The transcriptional pattern of zen during the early development.
But how does zen obtain its unique transcriptional
pattern? Figure 2 shows a set of pictures taken from
BDGP. It clearly shows the pattern of zen during the
nuclear cycle 4-6 of embryonic development, which
is occupied in the amnioserosa, dorsal ectoderm,
lateral ectoderm region. Zelda is translated by the
gene CG12701, a ubiquitous gene that switches off at
cycle 14, before cellularization (Gilbert 2000). As
mentioned previously, the expression of zen is
controlled by zelda extensively, with zelda mutation
comes no body formation in the transcriptional
region. However, zelda is a ubiquitously expressed
protein, whereas the expression of zen is only limited
to the amnioserosa, dorsal ectoderm, lateral ectoderm
ICBEB 2022 - The International Conference on Biomedical Engineering and Bioinformatics
of the embryo, so there must be something else that is
repressing zen during the development. This
something turns out to be one of the most important
maternally-expressed genes: dorsal (DI). The dorsal
gradient in the blastoderm embryo, through modeling
and experimental studies, was shown to be caused by
Cactus complex. This gradient is very important in
the early development. Where dorsal concentration is
highest, it switches on twi and sna, these two genes
code for transcription factor that represses brk, and
sog in the middle region of the embryo, where the
concentration of dorsal is significantly lower than the
bottom region but high enough to represses
decapentaplegic(dpp) and zen in the upper region,
where the dorsal concentration is zero. Brk and sog
are also responsible for repressing dpp and zen. Dpp
is a gene belonging to the TGF-β superfamily, which
gives rise to a series of signal translocation passway
all the way down to the specific target genes. Dpp
regulates the gene zen via the receptor-regulated Mad
protein. Table 3 represents a JASPER result (note that
I also highlighted zelda and dorsal, and the
CAGGTAG sequence, to further suggest the
importance of zelda) which I found out that the
transcription factor Mad binds very close to the
enhancer site of zen--it is only about 50 base pairs
away and have a relative high binding score,
suggesting that dpp is responsible for the regulation
of zen because Mad helps translocating its signal to
the gene zen. Furthermore, from the figure we can see
many dorsal (represented by symbol dl) binding sites,
suggesting that dorsal is repressing zen extensively in
the middle region of the embryo.
Table 3: The JASPER result of zen at the enhancer site(range selected: 200 base pair).
Name Score Relative
Start End
Predicted sequence
14.3542 0.9660256 124 134 + GATCATAAAAC
14.009 0.9614392 82 92 + TGCCATAAAAT
Stat92E 12.951 0.8955322 24 38 - AAGATTTTCGGGAAA
vfl 12.8612 0.9739354 162 173 - TTTCAGGTAGGT
11.9366 0.9061524 244 258 + GGGGCGCCGCCAGGC
fkh 11.8268 0.9307487 153 163 + TGTTTATTCAC
twi 11.7513 0.9311181 71 81 + TCACACATGCC
dl 11.0919 0.8878104 19 30 + CTGGTTTTCCCG
Hsf 10.9239 0.8929197 23 34 + TTTTCCCGAAAA
1 10.8339 0.9150343 5 15 - CTGTTTTCGTT
10.644 0.8938483 19 28 + CTGGTTTTCC
10.5191 1 396 401 - TAATCC
10.4822 1 57 63 + TTTATTG
dl 10.3655 0.8695819 342 353 + TGGGTTTCTCCC
hsf 10.3373 0.8803307 297 308 + AAATCCAGAAGT
“+stands for up-strand, “-stands for down-strand
The patterning genes are yet more fabulous than
you probably think. A large-scale genetic screen has
shown that many genes during the early development
can be classified into four categories, which are,
respectively, egg-polarity genes, gap genes, pair-rule
genes, and segment polarity genes. The highest
concentration of bicoid is located at the anterior of the
embryo, and gradually fades off towards the
posterior. Bicoid is encoded by a maternal effect gene
that produces mRNAs placed in certain regions of the
embryo. Consequently, bicoid is classified as an egg-
polarity gene because it is expressed in the anterior of
the embryo. This special patterning must have a
reason for its existence.
Bicoid is responsible for the formation of the head
because it is mostly concentrated at the anterior of the
embryo. And as mentioned previously, the mutation
of bicoid can bring death to the larva even before its
birth because the larva will not form a head. But what
keeps the bicoid in its limited region? In 1988,
Christiane Nüsslein-Volhard (who later won the
noble prize for her discovery of the anterior-posterior
polarity of early development of Drosophila) found
out that two genes, exuperantia and swallow, are
responsible for repressing bicoid, and with the
mutation of these two genes comes the diffusion of
bicoid further to the posterior region.
The Effect of the Transcription Factors Zelda, Dorsal, and Bicoid on the Pattern Formation of Drosophile Melanogaster during the Early
Bicoid also activates the adjacent gene
hunchback, a zygotic gene responsible for the
formation of thorax, as bicoid is developing (the
hunchback concentration appears at about 2 hours of
development). Hunchback is considered as a gap
gene because it is in gap with another gene
(information not shown). Bicoid also turns on the
genes giant and Krüppel, which are yet another two
examples of zygotic gap genes (for more information
about bicoid, see Bicoid gradient formation and
function in the Drosophila pre-syncytial blastoderm,
by Zehra Ali-Murthy and Thomas B Kornberg,
2016). And all these above-mentioned genes have an
impact on the formation of pair-rule genes. For
example, the stripe gene eve is activated by bicoid
and hunchback, whereas Krüppel and giant represses
it, keeping it limited in the stripe region.
The transcription factor zelda plays an important role
in the embryonic development of fruit fly. It is first
translated by the maternal gene and later replaced by
the zygotic ones. The mutation of maternal gene
translating zelda is fatal because the embryo lacks the
transcription factor zelda to regulate the gene
expression. The greatest affinity for zelda is
CAGGTAG, and it is shown to appear on both
promoter and enhancer sites of many pre-celluar
genes. And the lack of binding on either of these two
sites can bring to the non-transcription of the gene
and the abnormal body formation.
Dorsal is a maternally-expressed gene. It
establishes a gradient where it is mostly concentrated
at the bottom of the embryo and none at the top of the
embryo. This gradient helps establish the specified
transcriptional pattern, because it both activates and
represses genes, and these genes that are activated or
repressed also activate and repress each other,
limiting each other in the specific region.
Similar to dorsal, bicoid also activates and
represses certain genes and establishes the specified
transcriptional pattern. It establishes the gradient
where it is mostly concentrated at the anterior region,
and gradually fades off towards the posterior region.
Unlike dorsal, bicoid has a more profound effect
because it is the premise for the later formation of gap
genes, pair-rule genes, and segment polarity genes
since these genes that are activated or repressed by
bicoid also interact with each other in certain ways(I
did not talk about segment polarity genes because it
happens in the late stage of development).
Besides the information covered in this paper,
there are many other aspects of Drosophila that are
also being studied by scientists extensively.
Consequently, understanding Drosophila is a big
giant in the field of biology, and will no doubt receive
more attention in the future.
Alberts B, Johnson A, Lewis J, at al. (2002). Drosophila
and the Molecular Genetics of Pattern Formation:
Genesis of the Body Plan.
Carrell, S. N., O'Connell, M. D., Jacobsen, T., Pomeroy, A.
E., Hayes, S. M. and Reeves, G. T. (2017). A facilitated
diffusion mechanism establishes the Drosophila Dorsal
Eisen M., (2011). Zelda (the coolest transcription factor
ever) is a master regulator of embryonic adolescence.
Gilbert SF. (2000). The origins of Anterior-posterior
Liang H., Nien C.Y., [...], and Rushlow C. (2008). The zinc-
finger protein Zelda is a key activator of the early
zygotic genome in Drosophila.
Rushlow C., Pamela F. Colosimo, and Kirov. N. (2001).
Transcriptional regulation of the Drosophila gene zen
by competing Smad and Brinker inputs.
Tadros W., Howard D. Lipshitz. (2009). The maternal-to-
zygotic transition: a play in two acts.
Zehra Ali-Murthy, Thomas B Kornberg. (2016). Bicoid
gradient formation and function in the Drosophila pre-
syncytial blastoderm.
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