VEST 1 Flashcards
The addition of a 5’ end 7-methyl G cap to mRNA protects it from degradation by _________.
5’ exonucleases
The 5’ end 7-methyl G cap enhances the _________ of the 5’ most exon.
splicing
the ________ is necessary for targeting mRNAs for export to the cytoplasm through the nuclear pores.
5’ end 7-methyl g cap
In the cytoplasm, the 5’ end 7-methyl G cap interacts with ___________ to form a closed loop structure.
poly(A) tail binding proteins (at the 3’ end)
The closed loop structure formed by the 5’ end 7-methyl G cap and poly(A) tail binding proteins recruits the ________ for translation.
ribosome
RNA methylation to form N6-methyladenosine (m6A) in pre-mRNA is an abundant internal modification that controls ____________.
gene expression
The process of RNA methylation to form N6-methyladenosine (m6A) is referred to as the ______________.
epitranscriptome
m6A is found in mRNAs involved with specific _________ and __________.
developmental processes, cell differentiation
Most m6A sites are ________ and are similar in different tissues.
constitutive
m6A is enriched in the __________ and near _______, but also occurs in the _______ and internally.
3’ UTR and near stop codons, 5’UTR
The presence of a __________ is a strong inducer of m6A addition in the transcribed mRNA.
long internal exon
m6A addition occurs in the ________ during __________.
nucleus, transcription
The m6A writer complex adds the m6A _________.
co-transcriptionally
The m6A writer complex contains _________ and ________ proteins.
METTL3, METTL14
m6A erasers are mostly found in the _________.
nucleus
The main m6A eraser is __________.
ALKBHS
In the nucleus, the m6A binds “________”.
reader proteins
In the cytoplasm, other “reader proteins” affect ____________.
mRNA stability, localization,
and translation of the mRNA
_________ is the regulated removal of intron sequences from pre-mRNA.
Splicing
Splicing involves the simultaneous joining (________) of exon sequences together.
ligation
Exon sequences contain the _______________________.
5’ untranslated regions (UTR), protein coding regions, and the 3’ UTR
________ sequences are exported from the nucleus.
Exon
__________ is catalyzed by RNA.
Splicing
Pre-mRNA splicing uses the same chemistry as __________ but needs more help.
group 2 self-splicing
___________ is the most common type of splicing.
Protein-mediated splicing
Protein-mediated splicing needs _______ and ________ to perform the reactions.
proteins, RNA-protein complexes
_________ occurs when transcripts from different genes are spliced together.
Trans-splicing
Splicing is a highly regulated process that is necessary to remove ________ from the primary transcript.
RNA intron sequences
Both ________ and the primary pre-mRNA transcript have both exon and intron sequences.
genes (DNA)
Splicing removes the _________ to produce mRNA.
intron sequences
The gene includes DNA sequence that codes for all _________________________________________________.
all exons, introns, and those
sequences at the beginning and end of the RNA that are not translated into a protein,
including the entire transcription unit
The entire transcription unit includes _______________.
the promoter, the RNA coding sequence, and the terminator.
Sequences that direct where splices are made are surprisingly _______-.
simple
Splicing sequences include the _________.
5’ splice site, 3’ splice site, polypyrimidine tract, and branch point
The 5’ splice site splicing consensus sequence is ___________.
GU A/G AGU
The 3’ splice site splicing consensus sequence is ________.
CAGG
The branch point splicing consensus sequence is an ___________ approximately 18-40 nucleotides upstream from the 3’ splice site.
adenine (A)
The polypyrimidine tract splicing consensus sequence is approximately 10-20 _______ nucleotides.
C/U
The spliceosome is comprised of 5 ________ containing ____________.
RNA-protein molecules, small nucleolar RNAs (snRNPs)
The spliceosome contains up to ________ accessory proteins.
300
The _________ binds to the 5’ splice site.
U1 snRNP
The ________ binds to the branchpoint.
U2 snRNP
The ________ holds the 5’ and 3’ exons in close proximity to each other.
U5 snRNP
The _______ interact near the branchpoint.
U4-U6 snRNPs
The __________ binds the polypyrimidine tract and helps U2 bind to the branchpoint.
U2AF (U2 associated factor)
The U2AF also interacts with the ________.
3’ splice site
In addition to the snRNPs, there are at least _____, and perhaps up to ______, additional proteins that comprise the spliceosome and participate in the
splicing reaction.
24, 300
Following the release of _______, the 5’ splice site is correctly positioned in the active site due to base pairing between the 5’ end of the intron, the RNA
sequences in U6 snRNP, and interactions with U2 snRNP.
U1 snRNP
U2AF is composed of _____ subunits.
2
The ________ subunit of U2AF binds the polypyrimidine tract.
U2AF-65
The _______ subunit of U2AF binds the AG in the 3’ splice site.
U2AF-35
Together U2AF-65 and U2AF-35 recruit _________ to the branchpoint.
U2 snRNP
_______ also plays a critical role in positioning the 5’ and 3’ splice sites in the spliceosomal complex.
U5 snRNP
Just prior to lariat formation, _____________ all interact with each other to correctly position the RNA substrate for the splicing reaction.
U2, U5, and U6 snRNPs
_________ is a process where some exons are skipped and removed from the final mRNA product.
Alternative splicing
If something prevents default sequential splicing, then ________ will occur.
alternative splicing
Different proteins from the same primary RNA transcript can have markedly _________.
different functions
A major deciding factor in alternative splicing and differential protein production is ____________ binding to an RNA G quadruplex near the 5’SS.
RBM25
___________ elements are recognized by activator proteins.
Enhancer
__________ elements are bound by repressor proteins, which tend to be members of the ____________ protein family.
Silencer, hnRNP
Examples of hnRNP proteins include __________.
HNRNPI, HNRNPA1,
HNRNPC
Activators tend to enhance the binding of ________ to the regulated splice site, while repressors tend to inhibit binding or function of the ___________.
spliceosomal components
The binding of activator and repressor factors can occur in either ___________ or _________ sequences.
exon, intron
Alternative splicing is accomplished by regulating the ________ of sequences that direct where splices are made.
accessibility
_________ stands for exonic splicing enhancer.
ESE
________ stands for intronic splicing silencer.
ISS
_______ stands for intronic splicing enhancer.
ISE
_________ stands for exonic splicing silencer.
ESS
True or False: There are many forms of alternative splicing.
True
Polyadenylation requires ________ proteins.
50
The _______ sequence is canonically AAUAAA.
Polyadenylation Sequence (PAS)
__________ binds the AAUAAA sequence.
CPSF (Cleavage and Polyadenylation Specificity Factor)
_____________ binds the GU-rich or U-rich downstream element.
CSTF (Cleavage Stimulatory Factor)
CPSF and CSTF interact and along with additional cleavage factors, cut the ________.
pre-mRNA
__________ adds Adenines (A residues) to the 3’ end of the pre-mRNA.
PAP (poly-A polymerase)
The nuclear _________ binds to the 3’ end of the pre-mRNA.
Poly-A binding protein (PABPN1)
CPSF has ______ subunits.
4
CPSF 4 directly contacts the _____________ and recruits Poly A polymerase to the 3’ end.
PAS (AAUAAA)
CSTF has _____ subunits and binds the U/GU-rich element downstream from both the PAS and cleavage site.
3
CSTF is required for _________ but not _________-.
cleavage, polyadenylation
There are _____ CF factors that enhance 3’ end processing and cleavage at the 3’ end.
3
___________ is a scaffold for cleavage and polyadenylation machinery.
SYMPK (symplekin)
____________ is a member of the CPSF complex that interacts with and stimulates the activity of PAP.
FIP1L1
________ is a member of the CPSF complex that recognizes the PAS.
WDR33
The end to which polyA is to be added is generated by the _________ activity of _________.
endonuclease, CPSF2
The cleavage event produces _______ ends.
two
The 3’ end of the cleaved RNA gains a ________.
poly A tail
The 5’ end of the cleaved RNA recruits _________ or _______-.
XRN2, RAT1 (exonucleases that degrade the RNA)
When _________ or ____________ catch up with the RNA polymerase, they interact with the
polymerase C-Terminal Domain (CDT)) to cause it to cease transcribing the DNA
into RNA.
XRN2, RAT1
Cleavage of the RNA occurs approximately 15-30 nt downstream of the _______.
PAS
Poly A tail addition requires only __________.
PAP, CPSF, and PABPN1
Initially PAP ________ binds RNA and CPSF.
loosely
Regular dissociation of PAP only allows the addition of ________-.
a few A residues
Dissociation of PAP adding a few A residues is referred to as ___________.
distributive polyadenylation
__________ binding to short poly A sequences stabilizes PAP binding, leading to rapid addition of A residues without PAP dissociation.
PABPN1
PABPN1 binding to the short poly A sequence and rapidly adding more A residues is referred to as ___________.
processive polyadenylation
Most mammalian transcripts have a poly A tail of about _________ nucleotides.
200
The 3’ poly(A) tail protects the 3’ end from degradation by _________.
3’ exonucleases
The 3’ poly(A) tail is necessary for __________ from the nucleus to the cytoplasm.
mRNA transport
The 3’ poly(A) tail facilitates _________ by interacting with the 5’ cap.
translation
There is a link between ___________ and _________ of the 3’ terminal exon.
polyadenylation site proteins, splicing factors of the 3’
terminal exon
________ and other 3’ end processing proteins have been found to play a role in promoting alternative splicing at internal exon-intron junctions.
CPSF
Approximately _______% of mammalian mRNA contain more than one PAS.
75
Alternative PAS usage (_______) dictates the length of the transcript and its ___________.
alternative polyadenylation, stability, localization, and translation efficiency
Alternative polyadenylation may also impact the _________, leading to the translation of different protein isoforms.
coding sequence
Adding an extra 3 prime translated region to an mRNA adds a ___________ to the protein.
carboxy terminal domain
__________ are a subclass of RNAs that lack free 3’ and 5’ ends, thus existing as continuous loop RNAs.
Circular RNAs
CircRNAs have been identified for _____________ and are regulated in ________ and _______.
thousands of genes, developmental stages and pathological conditions
They are often expressed in a ________ manner.
tissue- or cell-type specific
CircRNAs are produced by a process called ________ of linear precursor RNAs.
backsplicing
CircRNAs are evolutionarily _______ and are found in flies through mammals, including humans.
conserved
At least _______ circRNAs are thought to exist in humans.
32
It has been postulated that _________ of RNA circRNA transcripts exist.
millions
CircRNAs may serve as _______ for certain diseases.
biomarkers
Examples of diseases for which circRNAs may serve as biomarkers include _________.
numerous cancers,
cardiovascular and neurological diseases
When splice sites (ss) are joined in a linear order by the pre-mRNA splicing machinery, a canonical _________ is generated that is also capped and polyadenylated.
linear mRNA
Alternatively, __________ can join a 5′ ss to an upstream 3′ ss, resulting in
production of a circular RNA whose ends
are covalently linked by a 3′-5′
phosphodiester bond and can function via a
number of distinct molecular mechanisms.
backsplicing
The ends of circular RNA are covalently linked by a _________.
3′-5′ phosphodiester bond
Primary functions of circRNA include acting as ________ and _________.
miRNA sponges, protein sponges, encode novel proteins
CircRNA can also ________ using alternative translation initiation mechanisms, such as IRES and m6A residues.
encode novel proteins
________ gives rise to circRNAs from lariat intermediate structures, which are produced during exon skipping.
Lariat-driven circularization
__________ is a more direct form of circRNA formation and involves hybridization of flanking introns, which brings splice sites in close proximity.
Intron-pairing-driven
circularization
A _______ consists of all exon sequence.
circRNA
A _________ consists of all intron RNA.
ciRNA
An _______ consists of exon and intron RNA.
EIciRNA
A 5’ methyl G cap is added to the pre-mRNA during ____________ to protect against 5’ degradation and facilitate translation.
transcription
Internal methylation in RNA can influence ______, _______, and _________.
stability, splicing, translation
The ________ (primary transcript) consists of exon (5’ UTR, protein coding region, 3’
UTR) and intron sequences.
pre-mRNA
________ occurs to remove intron sequences from the primary transcript.
Splicing
Polymerase II transcripts need _______ (snRNA + specific protein complexes) to splice out introns.
snRNPs
________ binds to the 5’ splice site.
snRNP 1
_______ binds to the branchpoint.
snRNP 2
_______ binds to the polypyrimidine tract.
U2AF
__________ generates multiple mRNAs and proteins from a single primary transcript.
Alternative splicing
The poly(A) tail consists of ~ _____- A residues and has multiple functions, including protecting the mRNA from 3’ degradation and enhancing translation.
200
________ are circular RNAs that regulate expression in multiple ways.
circRNAs
________ are noncoding sequences that interrupt the coding sequences (exons) of genes.
Introns
Introns are common in ________, but very rare in _________.
eukaryotic cells, bacterial cells
An mRNA molecule has 3 primary regions: a ________, a_______, and a ________.
a 5’ untranslated region, a protein
coding region, and a 3’ untranslated region
_________ is translated immediately after transcription and undergoes little processing.
Bacterial mRNA
The pre-mRNA of a eukaryotic protein-encoding gene is extensively processed in the following ways: (1) a modified guanine nucleotide and methyl groups, collectively termed a “ BLANK”, are added to the 5’ end of pre-mRNA; (2) introns are removed; and (3) the 3’
end is cleaved, and a poly(A) tail is added.
cap
Introns are removed from pre-mRNA within a structure called the _______, which is composed of several small nuclear RNAs and proteins.
spliceosome
Some pre-mRNAs undergo _________, in which different combinations of exons are spliced together, different promoters, and/or different 3’ cleavages sites
are used.
alternative processing
A cell can generate multiple mRNAs and multiple proteins through ____________.
alternative splicing
