Ch. 22 Post-transcriptional Regulation of Gene Expression in Eukaryotes

Question 1

What does alternate splicing produce?

Answer 1

Alternate splicing leads to the production of different polypeptides from a single pre-mRNA.

Question 2

How do eukaryotes regulate which exons are included or removed in alternate splicing?

Answer 2

Control of which exons get included or removed can be regulated by RNA-binding proteins that enhance or suppress splicing.

Question 3

What are examples of RNA-binding proteins that regulate exon removal or inclusion? (4)

Answer 3

Exonic splicing enhancers (ESE)
Exonic splicing silencers (ESS)
Intronic splicing enhancers (ISE)
Intronic splicing silencers (ISS)

Question 4

What are common protein families of RNA-binding proteins? (2)

Answer 4

Ser/Arg rich proteins (SR)
hnRNP

Question 5

What is alternate splicing involved in in fruit flies?

Answer 5

Involved in sex determination of fruit flies.

Question 6

What are U1/U2?

Answer 6

Ribonucleoproteins that perform splicing.

Question 7

What do some genes have in terms of transcriptional termination?

Answer 7

Some have alternative 3’ cleavage sites form transcriptional termination.

Question 8

Which cleavage site is used if multiple are available?

Answer 8

The cleavage site used is dependent on which proteins are present in the nucleus.

Question 9

What do alternate 3’ cleavage sites allow for?

Answer 9

Allows for C-terminus variation in polypeptides produced from a gene.

Question 10

What are alternative 3’ cleavage sites involved in?

Answer 10

The production of membrane-bound vs secreted forms of antibodies.

Question 11

What does phosphorylation of elF2-GDP do during translation?

Answer 11

It prevents loading of an initiator tRNA into the small ribosomal subunit.

Question 12

What needs to happen to elF2-GDP for translation to occur?

Answer 12

elF2-GDP will block all translation in a cell unless a signal is received that leads to its dephosphorylation.

Question 13

What are two uses for controlling translation with elF2-GDP-P?

Answer 13

1. used in red blood cell production of globin when heme is present
2. used to shut down translation in virally-infected cells

Question 14

Why is mRNA circularized?

Answer 14

Due to 3’ and 5’ end interactions

Question 15

Why is circularization of mRNA required?

Answer 15

Circularization is required for association of ribosomal small subunits and IFs

Question 16

How can circularization be inhibited?

Answer 16

By proteins that prevent interaction of IFs with other proteins.

Question 17

How can circularization inhibition by regulatory proteins be removed? (What does this mean?)

Answer 17

Modifications to the inhibiting proteins allows for proper interactions between IFs and other proteins. (This means it can be turned on and off.)

Question 18

What are upstream open reading frames (uORFs)?

Answer 18

Short reading frames upstream of a gene.

Question 19

How do uORFs impact ribosome binding?

Answer 19

The AUG of the uORFs competitively bind ribosomal subunits to reduce the likelihood of translation of the gene.

Question 20

What happens if a ribosome binds a uORF instead of an ORF?

Answer 20

The ribosome will hit the stop codon of the uORF and dissociate, meaning that ribosomes don’t form on the gene.

Question 21

How can cells overcome uORFs?

Answer 21

Phosphorylation of elF2ɑ reduces translation initiation, allowing the ribosome to pass the uORF AUGs to reach the gene AUG. (transcription of the gene is now more likely)

Question 22

What does mRNA degradation do for regulation?

Answer 22

mRNA degradation reduces the amount of mRNA for a gene available for translation.

Question 23

What does mRNA degradation begin with? (2)

Answer 23

Begins with removing the 3’ poly(A) tail and then removing the 5’ cap. This is done by enzyme complexes called P bodies.

Question 24

What happens once the poly(A) tail and 5’ cap are removed from mRNA?

Answer 24

The mRNA can be degraded by nucleases.

Question 25

Where is research shifting in terms of regulation of gene expression?

Answer 25

It is shifting to focus on how whole networks of genes are controlled and how they function together in cells and organisms (systems biology).

Question 26

How has nutrient availability been shown to impact pre-mRNA splicing?

Answer 26

Research shows that ribosomal pre-mRNA splicing is REDUCED during nutrient limitation, but the mechanism for targeting these specific mRNAs but not others is unknown.

Question 27

What does the phenomenon of nutrient limitation leading to reduced splicing suggest?

Answer 27

That splicing regulation provides a way to rapidly respond to environmental signals.

Question 28

What is a current hypothesis regarding splicing and introns?

Answer 28

Nutrient availability impacting mRNA splicing MAY be a reason for the evolution and maintenance of introns in eukaryotic genes.

Question 29

How to untranslated regions of genes impact regulation?

Answer 29

Untranslated regions coordinate translation of multiple mRNAs.

Question 30

What does iron homeostasis do and how is it regulated?

Answer 30

Iron homeostasis maintains appropriate iron levels in cells. It is controlled by untranslated regions.

Question 31

What are iron response proteins?

Answer 31

IRPs: bind untranslated regions (UTR) and affect translation.

Question 32

What do low iron levels lead to? (2)

Answer 32

1. blocked translation of proteins that use iron 1. increased translation of proteins that facilitate iron uptake

Question 33

What are conserved A-U rich elements?

Answer 33

conserved AREs control global RNA stability and are controlled by untranslated regions.

Question 34

What does the presence of an ARE in the 3' untranslated regions cause?

Answer 34

It leads to faster degradation (reduced stability of RNA).

Question 35

What are conserved AREs associated with? (5)

Answer 35

Proteins that regulate cell growth and responses to environmental stimuli, infection, and inflammation.

Question 36

What is RNA interference (RNAi)?

Answer 36

The interaction of RNA with mRNA to INHIBIT gene expression.

Question 37

What are the two types of RNAi?

Answer 37

Short interfering RNAs (siRNA) and micro RNAs (miRNA).

Question 38

What are siRNAs?

Answer 38

21-27 base RNAs produced by viruses that inhibit host gene expression.

Question 39

What are miRNAs?

Answer 39

Similar to siRNA, but are produced by the cell to regulate gene expression.

Question 40

Where does RNAi pairing often occur and what does it cause?

Answer 40

Pairing often occurs with the 3' UTR of mRNA, resulting in degradation OR translation inhibition.

Question 41

What is RNAi involved in? (2)

Answer 41

Involved in developmental timing and protection against RNA viruses.

Question 42

What is the process of miRNA formation? (4)

Answer 42

1. Transcribed from DNA sequences in the genome as pri-miRNA (primary miRNA) and cleaved by Drosha 2. Short hairpins called pre-miRNAs are produced and exported from the nucleus 3. Processed by Dicer which cuts the loop of the hairpin 4. dsRNA is separated by a helicase to produce mature miRNA

Question 43

How do miRNAs target and inhibit mRNA? (1, 2, 3a, 3b)

Answer 43

1. miRNA binds to complementary mRNA in the cytoplasm 2. dsRNA is targeted by RNA-induced silencing complexes (RISCs) 3. a)RISCs may block translation in animals or b)cleave the mRNA in plants

Question 44

How common is miRNA and why is it significant?

Answer 44

miRNA genes make up 4% of human genes, and a single miRNA may target up to 400 different mRNAs!

Question 45

How does siRNA protect against viral infections? (3)

Answer 45

Long dsRNA may be present during viral infections... 1. RISC/Dicer cleaves the dsRNA to shorter pieces 2. dsRNA strands are separated 3. siRNA interacts with mRNA in the cytoplasm

Question 46

What is the outcome of siRNA? (2)

Answer 46

RNA may be degraded, or translation may be inhibited.

Question 47

How is RNAi useful as a molecular technique?

Answer 47

It is useful in studying protein function because you don't need to knock out genes and stop protein production (potentially killing the cell).

Question 48

How does RNAi work to study protein function?

Answer 48

With RNAi, a small RNA can be expressed temporarily and knock out protein expression, allowing phenotypic studies to be performed.

Question 49

How is RNAi less lethal than other methods to study protein function?

Answer 49

The expression of the RNA can be turned off in the cell to allow normal protein production and reduce lethality.

Question 50

What does early development of fruit flies depend on? (2)

Answer 50

1. maternal mRNA gradients 2. regulatory gene expression

Question 51

What happens in early stages of fruit fly development?

Answer 51

At early stages, polarity occurs and results in anterior/posterior ends and dorsal/ventral surfaces.

Question 52

What happens after polarity occurs in fruit fly development?

Answer 52

metamerism (segmentation) occurs and each segment develops into different appendages.

Question 53

How are polarity and metamerism controlled during development?

Answer 53

Genetically controlled by genes/proteins conserved in ALL animals.

Question 54

What are developmental genes typically involved in regulating? What are the two types/classes of regulation?

Answer 54

Typically involved in regulating other genes. 1. regulate temporal expression (timing) 2. regulate spacial expression (location)

Question 55

What happens as more specific genes are expressed in a developing organism/cell?

Answer 55

As more specific genes are expressed, the cell identity becomes more specialized.

Question 56

What are the three types of genes involved in development?

Answer 56

Maternal genes, segmentation genes, and homeotic genes.

Question 57

What are maternal genes?

Answer 57

Genes deposited by maternal cells. They provide most early proteins needed for development.

Question 58

When is maternal mRNA translated?

Answer 58

mRNA is not translated until fertilization.

Question 59

What are segmentation genes?

Answer 59

Genes that are transcribed after fertilization and affect formation of the body segments.

Question 60

What are homeotic genes?

Answer 60

Genes that specify organ and appendage formation for each body segment.

Question 61

What is the trend seen with homeotic genes in eukaryotes?

Answer 61

The gene sequence is conserved in multicellular eukaryotes, but copy number tends to increase with complexity. (fruit fly=1 cluster and mammals=4 clusters)

Question 62

What are Hox genes?

Answer 62

Homeotic genes

Question 63

What do Hox genes correspond to in fruit flies?

Answer 63

Each Hox gene corresponds to a particular embryonic segment and controls development in that part.

Question 64

What do mutations of Hox genes produce?

Answer 64

Mutations in Hox genes cause improper appendage development.

Question 65

What is Ubx?

Answer 65

A Hox gene that is 77,000 bp (but 73,000 bp are introns) that takes one hour to transcribe and is thought to be a timing mechanism.

Question 66

What is the variance in structures produced by Hox genes though to be related to?

Answer 66

Variance in structures produced by Hox genes (arms vs wings) is related to the genes regulated by Hox genes, not the Hox genes themselves.

Question 67

What is a consequence of differentiated cells not dividing?

Answer 67

Differentiated cells often not dividing means organ malfunctions and tissue loss are hard to fix because cells don't "reprogram" to replace the loss.

Question 68

How can organ malfunctions or tissue loss be replaced/treated?

Answer 68

Stem cells may be useful to regenerate damaged tissues or organs, but the question becomes embryonic stem cells (unethical?) or induced pluripotent adult stem cells (must understand gene regulation!).