Developmental Genetics

Almost there!

What is development?

• Regulated growth resulting from interaction of genome, cytoplasm, and environment

• Programmed sequence of events

• Usually not reversible

Differentiation:

• Aspect of development

• Forming different types of cells, organs, ect. through specific regulation of gene expression

How do different cell types arise?

stem cells can be differentiated into different cells

• they all have the same genome/genetic material but they act and look different

T/F: coloning is where you go back from a differentiated tissue, to a stem cell, and then back to a differentiated tissue again

true 

_______ shows that adult differentiated cells retain a complete set of genetic info

cloning

How does cloning work?

• you have an oocyte donor who donates the egg, but not the genetic material (empty egg)

• Then you have your nuclear donor (individual you are trying to clone) → used genetic info from udder cells (genetic material from udder cells removed)

• This is injected into donor cells 

• Then the recipient cell takes new DNA and does cell division to start forming the fetus 

• This fetus goes into the host of a different phenotype and then you get an individual that can be born 

• birth of a clone animal 

• Take a somatic cell to make it a stem cell and then put it into the new egg to form a fetus

Anterior

front

posterior

rear

Melanogaster (fruit fly)

• Goes through larval stages after fertilization

• In the egg before the larval stage it has segements! 

• In hours we have segmentation pattern in the embryo → we also have the lateral axis! 

What are the structures of the fly

Head- throax- abdoman

Early Drosophila Development

• Maternal Genes (Egg Polarity Genes) 

  • Mother’s genotype affects offspring phenotype 

  • Establish anterior/posterior and dorsal (top)/ ventral (bottom) polarity

  • Transcribed during egg development 

  • Translated after fertilization (what RNAs are available to be translated after fertilization 

• Segementation genes 

  • Affect the number and polarity of segments

    • Gap Genes

    • Pair Rule Genes

    • Segement Polarity Genes

• Homeotic genes

  • Determine the identity of each segment

Maternal Genes 

• Mother’s genotype affects offspring phenotype 

• Establish anterior/posterior and dorsal (top)/ ventral (bottom) polarity

• Transcribed during egg development 

• Translated after fertilization (what RNAs are available to be translated after fertilization 

Segmentation Genes

• Affect the number and polarity of segments

  • Gap Genes

  • Pair Rule Genes

  • Segement Polarity Genes

Maternal Genes: Anterior-Posterior Axis

• Bicoid mRNA is anchored at anterior (since the mother goes through oogenesis, she gets to determine what genes and transcripts are made and where they are located)

  • Bicoid mRNA is concentrated at the anterior region 

  • After fertilization, Bicoid mRNA is translated into Bicoid protein that diffuses from the anterior end. Farther from the source gets lighter and lighter! 

    • Forms a gradient 

Nanos mRNA is anchored at posterior end 

• Then fertilization occurs and the Nanos mRNA is translated into Nanos protein that diffuses away from the posterior end

• It gets lighter in color the further away it is

• Highest conc near the source of the RNA and the lowest conc farthest from the RNA

Bicoid

• Bicoid mRNA is anchored at anterior (since the mother goes through oogenesis, she gets to determine what genes and transcripts are made and where they are located)

  • Bicoid mRNA is concentrated at the anterior region 

  • After fertilization, Bicoid mRNA is translated into Bicoid protein that diffuses from the anterior end. Farther from the source gets lighter and lighter! 

    • Forms a gradient 

Nanos 

Nanos mRNA is anchored at posterior end 

• Then fertilization occurs and the Nanos mRNA is translated into Nanos protein that diffuses away from the posterior end

• It gets lighter in color the further away it is

• Highest conc near the source of the RNA and the lowest conc farthest from the RNA

Maternal effect gene

• mother’s nuclear genotype determines progeny phenotype 

• If you have a wild-type egg and a sperm from a mutant male = you get a heterozygote that is perfectly normal

  • You still have bicoid mRNA that is anchored in the anterior, that gets translated into bicoid protein and diffuses! 

  • You have an anterior region

• If you have a mutant male and a normal sperm = you get a heterozygote (same genotype) that is mutant phenotype

  • There is no functional bicoid available, so you do not form an anterior portion.

What would you get if you have a wild-type egg and a sperm from a mutant male?

• If you have a wild-type egg and a sperm from a mutant male = you get a heterozygote that is perfectly normal

  • You still have bicoid mRNA that is anchored in the anterior, that gets translated into bicoid protein and diffuses! 

  • You have an anterior region

If you have a mutant male and a normal sperm =

• you get a heterozygote (same genotype) that is mutant phenotype

  • There is no functional bicoid available, so you do not form an anterior portion.

Maternal Genes: Anterior-Posterior Axis

• Bicoid mRNA is anchored in the anterior region (high conc of bicoid mRNA)

• In the posterior region we have a high conc of nanos 

• Bicoid and nanos regulate zygotic translation of maternal genes hunchback and caudal 

  • This means they are expressed and translated after fertilization has occured 

Two other maternal effect genes = caudal and hunchback (these are in the oocyte (egg) and they are not anchored anywhere) 

• they are diffused evenly throughout the embryo 

• Bicoid and nanos regulate caudal and hunchback (but caudal and hunchback start evenly diffused)

What does Bicoid do?

• Bicoid protein in the anterior of the embryo 

• Represses caudal mRNA translation by binding to caudal mRNA 3’ UTR

  • Caudal protein acts as a transcription factor to regulate genes for differentiation of the posterior part of the embryo 

• Bicoid is supposed to direct anterior formation, it binds caudal mRNA and when it does this it reduces its translation. However, caudal is important because it acts as a transcription factor to regulate genes for regulation of posterior structures. 

  • It is preventing posterior structure

• Bicoid also stimulates hunchback expression by binding a transcription factor binding site upstream of hunchback 

  • Bicoid acts as a transcription factor to upregulate more expression of hunchback.

  • Hunchback protein is produced from its RNA and then acts as a transcription factor to regulate genes for differentiation in the anterior embryo

    • It turns on genes for the anterior portion!! This is how bicoid promotes anterior structure 

How does the bicoid protein promote the anterior structure?

• It also stimulates hunchback expression. 

• Hunchback acts as a transcription factor and regulates genes for differentiation in the anterior part of the embryo 

• Bicoid also represses the caudal mRNA by binding to caudal mRNA 3’UTR

• Bicoid promotes anterior structures by upregulating a transcription factor called hunchback and represses posterior structures by blocking expression of transcription factor for posterior region = caudal 

What does Nanos do?

Nanos mRNA is deposited in the posterior of egg. After

fertilization, it is translated and also has gradient along the anterior-posterior axis.

Nanos Inhibits Hunchback translation by causing degradation of

its mRNA causing anterior-posterior hunchback protein gradient. This region is for the posterior, so you want to shut down anterior development back here.

What inhibits Hunchback translation?

Nanos!!

• Nanos blocks translation of hunchback by binding to the RNA.

• Hunchback is supposed to make anterior features, but is repressed by Nanos. 

Developmental Network: Anterior Posterior Axis:

• Bicoid ——> hunchback ——> anterior structures 

• Bicoid —/ caudal ——> posterior structures 

Recap: 

• Bicoid is anchored in the anterior and is translated from mRNA into protein that diffuses down the cell

• It promotes expression of hunchback, hunchback is a transcription factor for the anterior region, so it makes anterior structures 

• Bicoid also blocks caudal! Caudal’s normal function is to promote posterior structures 

What does bicoid block?

Caudal which has a normal function of regulating the expression of genes for posterior structures. 

Nanos developmental network

• Nanos, when present, blocks the expression of hunchback! This means no anterior structures can form! 

Recap 

• Nanos is anchored in the posterior region mRNA and then it becomes a protein which diffuses into the embryo

After fertilization has occured, what are the 4 proteins for the fly like?

• The bicoid’s mRNA is anchored in what will be the anterior region, when it translates into a protein it diffuses from its source 

• The nanos’s mRNA is anchored in the posterior region, when it is translated into a protein it diffuses from the source 

• The hunchback is higher in the anterior region and low amounts by nanos 

• Caudal is in low amounts by Bicoid. Higher in the posterior regions 

Segmentation genes

• affect number and organization of segments 

• the proteins are going to be in different concentrations at different locations, but these turn on different genes because of this 

• transcribed after fertilization so NO MATERNAL EFFECT

• The bicoid/nanos gradient regulates these genes 

• Gap genes: divide embryo into broad segments  

• Pair-Rule Genes: Affect same part of the pattern in every other segment  

• Segment polarity genes: identify one portion of the segment → affect anterior and posterior polarity of each segment

What are gap genes

one of the segmentation genes (no maternal effect)

• divide embryo into broad segments  

Pair-Rule Genes 

• Affect same part of the pattern in every other segment  

  • Divides the broad segments into even finer ones 

Bicoid protein is present at the highest levels in the

anterior (remeber the gradient, most concentrated by the source)

Nanos protein is present at the highest levels in the

posterior

Segment polarity genes

How we identify a section of the segment 

• affect anterior/posterior polarity of each segment 

Segmentation genes process

• hunchback is a maternal affect gene that promoted anterior structures 

• hunchback acts as a transcription factor and turns on a gap gene called knirps. 

  • Knirps acts as a transcription factor for evenskip → it is a pair-rule gene so we went from large to smaller segments. Now even skipped acts as a transcription factor for segment polarity gene (engrailed) → now each segment (the anterior or posterior part is identified). 

• We start with maternal effect genes that turn on the segment genes via a cascade of events 

Homeotic gene

• give specific identity to each segment 

• 2 major gene clusters in Drosophila 

  • antennapedia complex (head) and anterior thorax

  • bithorax complex: posterior thorax and abdomen 

  • all on same chromosome 

  • genes in order from anterior to posterior 

  • Each gene is only expressed in specific segments based on all of the concentrations of transcription factors before it!

Bithorax complex

• posterior thorax and abdomen 

T/F: the order of the genes along the chromosome match the order of expression along the embryo

true!!!! 

What do Homeotic genes do?

They are master regulator transcription factors

• they turn on the genes to make the structures that the cells need

Homeotic gene expression in Drosophila 

• where we had expression of anterior regions in the larval stage has the same genes present in the adult 

• The order of expression stays the same from larva to adult 

T/F: when you delete Ubx of the fly you extend the anterior portion which allows extra wings

true!

• Diffusion of the genes that make the anterior region 

T/F: homeotic gene is supposed to decide what structure is generated

true

Proteins containing the homeodomain are _______proteins. The homeodomain binds to specific DNA sequences and is thought to regulate transcription (they are transcription factors)

DNA binding 

• in flies, we had one suite of homeotic gene on one chromosome 

T/F: most animals have homeotic genes?

true!

C. elegans

• transparent organism so you can see cell divisions 

• can track differentiation of every cell 

Apoptosis

• programmed cell death to give normal phenotype 

• Cell death is an important aspect of development 

  • Removal of tissue between fingers: if this doesn’t happen, then you can have webbing.

  • creation of joints: to move they need to be independent structures 

  • neural pruning: in the process of brain development, neurons are generated in extra amounts, but they can create less than functional results. 

    • Only the neurons that made the best connections are the ones that are kept. 

    • In a mature fiber, most of the neurons that initally started have been killed off and the best connections remain. Only the junctions with the highest potential. 

Flower development of Arabidopsis

4 concentric whorls 

• Sepals are on the outermost part 

• petals 

• stamen 

• carpel (stamens release pollen here to fertilize the eggs)

The ABC Model

The A, B, and C genes make transcription factors which bind to the

DNA to allow transcription of specific genes and at specific times of

development.

• in these whorls we get expressions of different classes of homeotic genes. These genes make transcription factors and they bind to other specific genes at certain times of development to make different structures 

  • Homeotic genes are transcription factors that direct the expression of genes necessary to make structures 

In whorl one we have expressions of only

A genes

In whorl 2

expression of A and B and this makes petals

In whorl 3

we have B and C class expression and that makes stamens

In whorl 4 or inner most

carples only for class C

The classes are antagonists to each other….

wherever you get C you dont get A

• wherever you get A you dont get C

• trying to block each other 

A Class Mutant

• Whorl 1: mutant 

• Whorl 2: Mutant 

• Whorl 3: Stamen 

• Whorl 4: Carpel

• mutant A means A is not expressed, and C gets to spread all throughout the whorls because A would battle C ( A usually represses C)

• 3 and 4 are fine because they are in the C regions they have normal expression

B Class mutants

• these are ones where we expect expression to be across whorl 2 and 3, but if its gone, that means that they are mutants

• A by itself is sepals

• C by itself if carpals

• get something like sepal, sepal, carple, carple

If there is a mutation in the class C gene, the phenotye in which whorls would be altered

• whorl 3 = stamens

• whorl 4 = carpels

Class C gene _______ prevents more than 4 whorls

AGAMOUS

• So when it is mutant, varying number of whorls of petals and

sepals or a flower in a flower can develop.