1.5: Regulation of the Transcriptome

Question 1

what can transcriptome analysis provide

Answer 1

signature of cell state due to a response to extracellular stimuli or diseases states

Question 2

in testing for primary AML (acute myelogenous leukemia cells), what does the IC50 mean?

Answer 2

the IC50 is the [C] of compound required to inhibit cell proliferation by 50% thus a lower IC50 means a more effective compound

Question 3

can eukaryotic or prokaryotic chromosomes couple transcription or translation

Answer 3

prokaryotic bc it’s circular genomes and there’s no organelle separation

Question 4

eukaryotic __________ is tightly coupled to transcription

Answer 4

rna processing

Question 5

how to rna processing in eukaryotes tightly coupled to transcription

Answer 5

• covalent modifications of rna ends
• removal of intron sequences (even before transcription is fully complete)

Question 6

describe rna capping

Answer 6

addition of modified guanine nucleotide to 5’ end of pre mRNA (3 enzymes involved) and the cap is bound by cap binding complex (CBC)

Question 7

provide an example of a modification that you can do to protect from exonuclease (<- like a pacman)

Answer 7

add methyl groups

Question 8

what bonds do exonucleases cut

Answer 8

phosphodiester bonds (covalent)

Question 9

what are the functions of rna capping

Answer 9

1. hlps rna processing and export from the nucleus
2. important role in translation of mRNAs in the cytosol
3. protects mRNA from degradation

Question 10

eukaryotic genes are made up of coding sequences called _____ and non coding seq called __________

Answer 10

exons and introns

Question 11

both introns and exons are transcribed into rna, state the process of the removal of introns

Answer 11

rna splicing

Question 12

describe alternative splicing

Answer 12

different cells can splice an rna transcript differently to make proteins of the same gene

Question 13

how do our genes increase the coding potential of genomes

Answer 13

through alternative splicing, ~75% of human genes produce multiple proteins

Question 14

what does a spliceosome do

Answer 14

rna splicing, the spliceosome is an enzyme complex made up of rna and protein

Question 15

what can serve as a marker for properly spliced rna

Answer 15

sites of proper splicing are bound by exon junction complexes (EJCs)

Question 16

describe negative and positive controls of alternative splicing

Answer 16

negative control: default is splicing and no regulation. if there is a repressor the splicing is blocked.
positive control: default is no splicing through no regulation, the spliceosome doesn’t recognize the introns. the activator binds to its binding site and introns are removed.

Question 17

how are drosophilas sex determined

Answer 17

through ratio of X chromosomes to autosomal sets == X:A

Question 18

which ratios lead to the male and female drosophila

Answer 18

X:A = 0.5 Male
X:A = 1.0 Female

Question 19

what are the 3 genes involved into drosophila sex determination and what do they do

Answer 19

all 3 genes contain regulated splice sites.
- sex lethal: splicing repressor
- transformer: splicing activator
- double sex: regulates sex gene expression

Question 20

describe the splicing regulation in drosophila to get a male

Answer 20

sex lethal is not regulated and the splice product is non functional, the transfomer gene is not regulated and the splice produce is non functional. the regulated 3’ splice site is inactive and it gets cut. the double sex gene is not regulated so the Dsc protein leads to 400aa + 150 male specific aa and this represses female gene expression
— all genes are not regulated splicing

Question 21

describe the splicing regulation in drosophila to get a female

Answer 21

1st step: special cl produced that is functional when spliced — transient
there is a positive feedback loop of splicing bc the functional sxl protein is used to block the splice site and so a larger section is removed . the sxl protein is regulated and it represses splicing of scl and tra. tran has its splice site blocked and a larger region is removed. tra is regulated and activates the splicing of dsx. at the dsx gene, the functional tra protein and transformer 2 come together and leads to 400 aa + 30 female specific aa that represses male gene expression
– all genes have regulated splicing.

Question 22

during 3’ polyadenylation, what gets added to c terminal domain tail of rnap

Answer 22

CstF (cleavage stimulating factor)
CPSF (cleavage and polyadenylation specificity factor)

Question 23

go over 3’ polyadenylation and termination

Answer 23

rna cleaved, transcription terminates, poly a polymerase (PAP) adds ~200 A nucleotides to the 3’ end of RNA from ATP (the poly a tail is not genome encoded), the poly a tail is bound by poly a binding proteins which aid in rna export, translation and mRNA stability

Question 24

t/f the poly a binding proteins block 3’ exonucleases

Answer 24

yes

Question 25

Which of the following is typically true in Drosophila sex determination?
A. In males, Tra RNA is not spliced and functional Tra protein is produced.
B. In males, Tra RNA is not spliced and nonfunctional Tra protein is
produced.
C. In males, Tra RNA is spliced and functional Tra protein is produced.
D. In males, Tra RNA is spliced and nonfunctional Tra protein is produced.

Answer 25

D

Question 26

A scientist places high levels of a miRNA targeting Sxl RNA into all cells of
a developing Drosophila embryo. This results in Sxl RNA being specifically
and completely destroyed. No other RNAs are destroyed.
Which of the following will be observed?
A. The Drosophila will develop into a male.
B. The Drosophila will develop into a female.
C. The Drosophila will develop into a male only if the X:A ratio is 0.5.
D. The Drosophila will develop into a female only if the X:A ratio is 1.

Answer 26

A - in males, it is non func and the other rna will still work. in females, the prot wont work so you can get the sxl prot, the transformer step is now the same as male thus leading to male development