The Effect of the Transcription Factors Zelda, Dorsal, and Bicoid on

the Pattern Formation of Drosophile Melanogaster during the Early

Development

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

development.

1 INTRODUCTION

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,

MZT

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

646

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

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/+, +/+

normal

M/M

mutan

henotype

2 METHOD AND RESULT

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

Development

647

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

648

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

Score

Start End

Strand﹡

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

(

var.2

)

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

Development

649

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.

3 CONCLUSION

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.

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Alberts B, Johnson A, Lewis J, at al. (2002). Drosophila

and the Molecular Genetics of Pattern Formation:

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Carrell, S. N., O'Connell, M. D., Jacobsen, T., Pomeroy, A.

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diffusion mechanism establishes the Drosophila Dorsal

gradient.

https://journals.biologists.com/dev/artical/144/23/4450

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Eisen M., (2011). Zelda (the coolest transcription factor

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https://www,michaeleisen.org/blog/?P=617

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https://www.ncbi.nlm.nih.gov/books/NBK9983

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