1.5: Regulation of the Transcriptome Flashcards
what can transcriptome analysis provide
signature of cell state due to a response to extracellular stimuli or diseases states
in testing for primary AML (acute myelogenous leukemia cells), what does the IC50 mean?
the IC50 is the [C] of compound required to inhibit cell proliferation by 50% thus a lower IC50 means a more effective compound
can eukaryotic or prokaryotic chromosomes couple transcription or translation
prokaryotic bc it’s circular genomes and there’s no organelle separation
eukaryotic __________ is tightly coupled to transcription
rna processing
how to rna processing in eukaryotes tightly coupled to transcription
- covalent modifications of rna ends
- removal of intron sequences (even before transcription is fully complete)
describe rna capping
addition of modified guanine nucleotide to 5’ end of pre mRNA (3 enzymes involved) and the cap is bound by cap binding complex (CBC)
provide an example of a modification that you can do to protect from exonuclease (<- like a pacman)
add methyl groups
what bonds do exonucleases cut
phosphodiester bonds (covalent)
what are the functions of rna capping
- hlps rna processing and export from the nucleus
- important role in translation of mRNAs in the cytosol
- protects mRNA from degradation
eukaryotic genes are made up of coding sequences called _____ and non coding seq called __________
exons and introns
both introns and exons are transcribed into rna, state the process of the removal of introns
rna splicing
describe alternative splicing
different cells can splice an rna transcript differently to make proteins of the same gene
how do our genes increase the coding potential of genomes
through alternative splicing, ~75% of human genes produce multiple proteins
what does a spliceosome do
rna splicing, the spliceosome is an enzyme complex made up of rna and protein
what can serve as a marker for properly spliced rna
sites of proper splicing are bound by exon junction complexes (EJCs)
describe negative and positive controls of alternative splicing
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.
how are drosophilas sex determined
through ratio of X chromosomes to autosomal sets == X:A
which ratios lead to the male and female drosophila
X:A = 0.5 Male
X:A = 1.0 Female
what are the 3 genes involved into drosophila sex determination and what do they do
all 3 genes contain regulated splice sites.
- sex lethal: splicing repressor
- transformer: splicing activator
- double sex: regulates sex gene expression
describe the splicing regulation in drosophila to get a male
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
describe the splicing regulation in drosophila to get a female
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.
during 3’ polyadenylation, what gets added to c terminal domain tail of rnap
CstF (cleavage stimulating factor)
CPSF (cleavage and polyadenylation specificity factor)
go over 3’ polyadenylation and termination
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
t/f the poly a binding proteins block 3’ exonucleases
yes
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.
D
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.
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
