Exam 3 Flashcards
What are assays that determine RNA secondary structures?
RNAse Digestion
DMS-seq
SHAPE-seq
What are the assays that determine RNA abundance?
(q) RT-PCR
PT-PCR
RNA-seq
What is the assay that determines promoter/consensus sequences?
CHIP-seq
What is the assay that determines rate of transcription?
GRO-seq
What are the 3 enzymes used in RNAse digestion assay and what do they do?
RNAse V1: cleaves dsRNA
RNAse 1: cleaves ssRNA
RNAse T: cleaves ssRNA
If you were using RNAse V1 to determine the secondary structure what would you see on the gel if the temperature was high?
nothing: RNAse V1cleaves dsRNA so it would all be denatured
If you were using RNAse 1 to determine the secondary structure what would you see on the gel if the temperature was high?
everything: RNAse 1 cleaves ssRNA with would be all of the RNA at high temps
What is the modification of DMS-seq?
modify A and C in ssRNA
Is DMS-seq genome wide or sensitive?
genome wide
What is special about DMS-seq?
it can be done in vivo and in vitro
In DMS-seq where does the RT polymerase stop?
at all the modifications of the A and Cs
Are there DMS signals present at dsRNA in DMS-seq charts?
no; it only deals with ssRNA
DMS signals in DMS-seq represent what?
ssRNA
What is the most accurate assay at predicting RNA secondary structures?
SHAPE-seq
What is the modification of SHAPE-seq?
2’ OH on ssRNA
What is special about SHAPE-seq that makes it so specific?
single nucleotide resolution (observes each base)
SHAPE-seq and DMS-seq have the same mechanism but what 2 things are different about them?
- SHAPE-seq has single nucleotide resolution (more specific)
- different modifications
What RNA abundance assays are relatively quantitative?
(q) RT-PCR
RNA-seq
(q) RT-PCR and RT-PCR are the same except for what 2 things…
(q) RT-PCR is quantitative and measures every cycle while RT-PCR is not
(q) RT-PCR and RT-PCR is genome wide or sensitive?
sensitive
What RNA abundance assay uses fluorescence?
(q) RT-PCR
What is the equation in (q)RT-PCR to determine the fold of a sample?
2 ^ (cycle # - cycle #)
What RNA abundance assay is the most commonly used?
RNA-seq
Is RNA-seq genome wide or sensitive?
genome-wide
What assay can detect intron splicing?
RNA-seq
Why do you need the whole genome sequenced for RNA-seq?
you must be able to match the sequenced fragments to their location in the genome (aids in identification of splice sites)
What are the dips in RNA-seq charts represent?
introns/splicing
Is CHIP-seq genome wide or sensitive?
genome-wide
What does CHIP-seq use to tag RNA?
antibodies
what does CHIP-seq idenitfy?
location of proteins that bind to DNA (like sigma factor)
Why do you need the whole genome sequenced for CHIP-seq?
you need to be able to match the sequenced fragments that had the protein bound to it to its location in the genome
CHIP-seq chart shows letters at positions in the genome; what does this help identify?
consensus sequence
What is the modification in GRO-seq?
changing UTP to BrUTP
What does GRO-seq use to tag BrUTP?
antibodies
What assays use antibody tagging?
GRO-seq and CHIP-seq
Is GRO-seq genome wide or sensitive?
sensitive
What assay looks at strands being actively transcribed by RNA polymerase?
GRO-seq
What assay needs different adaptors added to each end of fragments and why?
GRO-seq
needed to identify the direction of transcription
What does the first positive peak in GRO-seq graphs show?
proximal pausing
What 3 things did GRO-seq discover?
- proximal pausing
- bi-direction transcription
- transcription (bi-directional) at enhancers even though they don’t code for anything
What 3 things are special to RNA making it less stable?
- 2’ OH
- single stranded
- uracil (incorrect base pairing)
How many hydrogen bonds does G-C, A-U and G-U have?
G-C: 3
A-U: 2
G-U: 2
Out of G-C, G-U and A-U what is their strength ranking?
G-C (strongest)
A-U
G-U (weakest)
What is the most common unusual base in RNA?
pseudouridine
unusual bases are most common in what RNAs?
tRNAs
What is the purpose of unusual bases in RNA?
increase stability
What RNA assays are sensitive and not genome wide
(q)RT-PCR
GRO-seq
What does Non-Watson-Crick base pairing triple helixes do to RNA?
increase stability
What is the difference between an internal loop or multi-loop in RNA secondary structure?
multi-loop has more than 2 branches coming off it
What is different about A form RNA?
shorter and fatter
What is an example of a G-quadruplex?
GGGG (telomeres)
Are secondary or tertiary RNA structures more stable?
secondary (lower free E)
What proves structure = function in RNA?
ncRNA secondary structure are more conserved than their sequences
______________ are ribonucleoproteins which guide RNA molecules to their appropriate destinations
signal recognition particles (SRP)
eukaryotic SRPs are made of _____ RNA
7SL
What is pRNA?
packaging RNA
What are ribozymes?
catalytic RNA
What do natural ribozymes do?
formation of peptide bonds
cleave phosphodiester bonds
What do artificial ribozymes do?
glycosidic bond formation
RNA phosphorylation
What happens if RNA is a ribozyme AND a riboswitch?
1 sequence with 2 structures with different functions
What are riboswitches?
sensitive to environmental changes
What are aptamers?
RNA that binds to specific ligands
What is special about RNA in the RNA v. Lipid world that show they were first?
store genetic information and catalytic reactions
What were the first enzymes?
ribozymes
what RNA was the first that lead to life?
self-replicating RNA
What is transcription?
RNA synthesized from DNA template
what performs transcription polymerization?
RNA polymerase
What are 3 similarities between RNA and DNA polymerase?
require a template
goes in 5’–3’
adds single nucleotides at a time
Does RNA polymerase require a primer?
No (DNA polymerase does)
Can transcription happen outside of S phase in prokaryotes?
yes
Is RNA or DNA polymerase more error prone?
RNA polymerase
Are transcription and translation coupled in eukaryotes?
No (it is in prokaryotes)
How many RNA polymerases does bacteria have?
1
How many subunits does bacterial RNA polymerase have?
5
What is the prokaryotic holoenzyme of RNA polymerase?
the active form of RNA polymerase (sigma factor bound)
What is not always attached to prokaryotic RNA polymerase?
sigma factor
What does the prokaryotic RNA polymerase sigma factor do?
directs polymerase to promoter
Do all prokaryotes have the same number of sigma factors?
No all different
Does bacterial RNA polymerase have a helicase?
No, uses Mg2+ isomerase to unwind DNA
What are the 4 steps of bacterial transcription initation?
- RNA pol sigma factor recognizes and binds to promoter (closed complex)
- DNA winds by Mg2+ isomerazation (open complex) transcription bubble
- first phosphodiester bond formed (unstable ternary complex)
- release of sigma factor (stable ternary complex)
0
0
Do sigma factors have to bind to exact consensus sequences?
No, they can vary slightly
Why is it beneficial for bacteria to have different variations of consensus sequences?
allows different levels of that genes expression and different times
The more the consensus sequence matches the original…
the stronger the binding of the sigma factor = more transcription
0
0
What specifically on the promoter does the sigma factor recognize?
consensus sequence
The _____ domain on bacterial RNA polymerase binds the UP element, thereby strengthening RNA Pol’s binding affinity to the promoter
alpha - CTD
Upstream promoters are present on ________ expressed genes
highly expressed genes
What does DNA footprinting identify?
RNA polymerase binding site (sigma factor)
What is abortive initiation in bacteria?
RNA polymerizes a few times but then it is stuck because sigma factor is still attaching it to promoter
What is promoter escape?
in abortive initiation polymerase is able to escape and polymerize because sigma factor released
in bacteria, _________ forms ahead and behind transcription bubble during elongation
positive supercoils
In bacteria, is transcription a smooth process?
No (proximal pausing)
What stalls RNA polymerase in transcription in bacteria?
strong GC stem loop
In bacterial Intrinsic termination, what causes the RNA polymerase to fall off and release transcript?
UUUUUUU
How does Rho-dependent termination in bacteria happen?
GC stem loop stalls polymerase, Rho factor catches up to polymerase, Rho melts off the transcript and polymerase
Why is post-transcriptional modification in bacteria rare?
transcription and translation coupled
What is a post-transcriptional modification in bacteria?
polyadenylation
Polyadenylation in bacteria _______ the mRNA while in eukaryotes it _______ it
bacteria - destabilizes
eukaryotes stabilizes it
All rRNA is derived from a single precursor in bacteria. Why is this possible?
rRNA is not translated into a protein so it has time to be modified into different types of rRNA
What degrades bacterial RNA?
endosomes and exosomes
Why is the polyA tail added to bacterial mRNA?
bacteria have hairpins at the end of mRNA so polyA allows exonucleases to degrade mRNA
What is constitutive gene expression?
expressed all the time
What is repressible gene expression?
normally off
What is inducible gene expression?
normally on