FAN Flashcards
The introduction of double stranded RNA (dsRNA) into a cell causes degradation of the ___________ mRNA.
complementary
RNA interference (RNAi) is a phenomenon in which the introduction of ________ into a diverse range of organisms and cell types causes degradation of the complementary mRNA, thereby specifically knocking down the expression of genes.
double-stranded RNA (dsRNA)
siRNA stands for _______.
small interfering RNA
Long dsRNAs are cleaved into short 21-25 nucleotide siRNAs by a ribonuclease known as _________.
Dicer-2
The siRNAs made by Dicer-2 assemble with protein components into a/an __________.
RNA-induced Silencing Complex (RISC)
Activated RISC then binds to the complementary transcript by _______ interactions between the siRNA strand and the mRNA.
base pairing
Sequence-specific degradation of mRNA results in ________.
gene silencing
Cell response to dsRNA is more complicated; it triggers a cellular immune response involving the release of ________ that ultimately kills the cell. This is an issue!
interferon
In 2001, it was discovered that if ________ are introduced into mammalian cells, they avoid the activation of cellar inflammation and death signaling; a gene-specific silencing process can be started.
small interfering RNAs (siRNAs) (<50 nt at the time; now usually 19-21nt)
The process for determining an effective siRNA has ____ rules.
5
The 5’ end of the antisense strand of a functional siRNA should have a/an _____ or _____.
A or U
The 5’ end of the sense strand of a functional siRNA should have a/an _____ or ______.
G or C
A functional siRNA should have greater than ______ A or U nucleotides in the seed sequence (second - ninth nt of antisense strand from the 5’ end).
4
The cleavage site (9-10 nt) of a functional siRNA should be an ____ and _____.
A/U
A functional siRNA should have ________ 2-nt 3’-overhangs.
unilateral
shRNA stands for ________.
short hairpin RNA
shRNA is used for _______ expressing double-stranded siRNA.
long-term
The spacer in shRNA is _________.
TCAAGAG
siRNA delivery is used in _____ and _______ research.
basic, clinical
Some applications of ______ include cancer, hypercholesterolemia, infections, developmental defects, and neurodegenerative diseases.
siRNA
In principle any gene can be silenced by ______.
small interfering RNAs (siRNAs)
RNAi provides a rapid approach for assessing the ________ and developing siRNA drug to treat human disease.
loss-of-gene function
Long dsRNA, synthetic dsRNA, and shRNA can be processed to siRNA via ________, then induce the sequence-specific degradation of complementary mRNA.
dicer
The phenomenon of RNA-mediated gene silencing is called ___________.
RNA interference (RNAi)
There are ______ major divisions of non-coding RNA (ncRNA).
2
The 2 types of ncRNA are _______ and _________.
housekeeping (snRNA, tRNA, rRNA), regulatory (RNAi, eRNA, lncRNA, etc)
A microRNA is a small non-coding RNA molecule containing about ______ nucleotides.
21-25
miRNA is found in plants, animals, some viruses, and ______.
humans
miRNA functions mostly in ________ and _________ regulation of gene expression.
RNA silencing, post-transcriptional
The first microRNA ______ was discovered in 1993.
lin-4
lin-4 produces a ______ nucleotide RNA.
~21
The lin-4 RNA contains sequences partially complementary to multiple sequences in the _______ of the lin-14 mRNA.
3’ UTR
The binding of lin-4 RNA to lin-14 mRNA causes the ______ of lin-14 mRNA translation.
inhibition
The second microRNA, ______, was discovered in 2000.
Let-7
miRNA genes are located in the _____ regions of the genome.
intergenic, intronic, exonic
The passenger strand of miRNA is also known as ________.
miRNA*
The guide strand of miRNA is also known as _______.
mature miRNA
The guide strand of miRNA forms the ______.
miRISC
The miRISC binds to the _______ of mRNA.
3’-UTR
RNA sequencing results show that _________ of a miRNA are expressed and functional.
both strands
The 2 strands of miRNA are named using the _______ nomenclature.
miR-name-number-letter p
The _______ of the miRNA name denotes which arm of the precursor hairpin the miRNA is derived from.
letter
miRNAs recognize their target mRNA 3’-UTR by the ________ rule.
Seed-Match
One miRNA can target _______ of multiple genes.
3-UTRs
One gene 3-UTR can be targeted by __________.
multiple miRNAs
A ______ assay is used to validate miRNA targets.
reporter
________ can be used to overexpress miRNA.
miRNA mimics
_______ can be used to reduce miRNA levels.
AntagomiR
AntagomiRs are modified with _______ and ________ to enhance stability.
2′-O-methyl-modified nucleotides, phosphorothioate linkage
MicroRNAs are a class of endogenous non–protein-coding RNAs comprising about ______ nucleotides.
22
miRNAs are well-conserved among _______.
species
miRNAs regulate gene expression at the _______ level.
post-transcriptional
miRNAs recognize their target ________ where they mainly inhibit translation or direct destructive cleavage of target mRNA.
mRNA-3’UTRs
One miRNA can regulate ______ or ______ of gene expression.
tens, hundreds
One gene expression can be regulated by ______ different miRNAs.
multiple
Long ncRNA is defined as transcripts that are produced by ________.
RNA polymerase II
Long ncRNA is defined as transcripts that are longer than ______ nucleotides.
200
Long ncRNA is defined as transcripts that are _______ conserved among species.
poorly
Long ncRNA can regulate gene expression either _______ or _________ at either the _______ or _______ level.
positively or negatively, transcriptional (nucleus) or post-transcriptional (cytosol)
All known lncRNAs are divided into _______ classes.
five
The 5 classes of lncRNAs are based on their relationship with ______ or _______ genomic features.
adjacent, overlapping
The 5 classes of lncRNAs are sense, intergenic, antisense, bidirectional, and ______.
intronic
________ lncRNAs are the most common.
Sense
_______ lncRNAs are the second most common.
Intergenic
lncRNAs mediate gene regulation in the ______ and the _______.
nucleus, cytosol
Long non-coding RNAs (lncRNAs) are RNA transcripts longer than ________ bases and without evident protein-coding capacity.
200
Most lncRNAs are ________ and their most common mechanism of action is via recruitment of blank to DNA.
nuclear
Some lncRNAs bind to specific proteins and act as ________ within ribonucleoprotein complexes.
scaffolds
In the cytosol, some lncRNAs can act at the post-transcriptional level as ______ for miRNAs therefore inhibiting the actions of miRNAs on mRNAs.
sponges
A circRNA is generated by covalently linked the _______ and _______ ends of RNA together to form a single-stranded continuous loop structure.
3’, 5’
CircRNAs are found in all ______ of life.
kingdoms
CircRNAs are _______ abundant in cells.
highly
CircRNAs are _________ conserved.
evolutionary
CircRNAs can be specific for certain _______ or ______ stages.
cell types, developmental stages
CircRNAs usually arise from _______ events and circularization of ______ or ______.
splicing, exons, introns
CircRNAs are _________ stable due to the lack of exposed ends.
extraordinary
Circular intronic RNAs are formed when an intron _______ resulting from exon skipping forms a circular structure.
lariat
Circular exonic RNAs are formed when _______ inverted repeats or ALU elements forms an extended base-paired structure.
flanking
Circular exonic RNAs are formed when interactions between _______ form a bridge.
RNA-binding proteins
Splicesome-mediated splicing joins a 5’ splice site of a downstream exon with a 3’ splice site of an upstream exon to yield a circular RNA with a “________” junction between exon 4 and exon 2.
scrambled exon
There are ________ tools available for the discovery of circRNAs from RNA sequencing datasets.
prediction
circRNAs can act as miRNA _______.
sponges
circRNAs can bind to ________.
cellular proteins
circRNAs can generate _________.
polypeptides
circRNAs can regulate __________ splicing, ______ transcription, and _______ translation.
alternative splicing, gene transcription, protein translation
circRNAs are a group of endogenous ncRNAs with a special covalent _________ structure.
closed loop
circRNAs do not have a 5-end _____ and 3- end ______ structure.
cap, poly(A) tail
circRNAs may arise from ________ or ________.
introns, exons
The formation of different types of circRNAs results in the formation of _______, ________, and ________ circRNAs.
exonic (ecircRNA), intronic (ciRNA), exon-intron (EIciRNA)
The vast majority of circRNAs particularly ________ dominantly accumulate in cytoplasm, and ________ and _________ are dominantly localized in the nucleus.
ecircRNAs, EIciRNAs and ciRNAs
Extracellular non-coding RNAs can be found in __________.
microvesicles
Extracellular non-coding RNAs can be found in _______, ________, ________, and ________.
exosomes, apoptotic bodies, proteins, body fluids
Extracellular non-coding RNAs can act as __________.
biomarkers
Extracellular non-coding RNAs can be used for ________ between cells.
communication
RNA interference is when the introduction of ________ into a cell causes degradation of the complementary mRNA.
double-stranded RNA
shRNAs are processed to become _________ in cells.
siRNAs
A functional siRNA should have a ____ or _____ at the 5’ end of the antisense strand.
A or U
miRNAs regulate protein expression by recognizing their target ________ and inhibiting translation or directing cleavage of the target.
mRNA-3’UTRs
lncRNAs regulate gene expression at the ________ or ________ level.
transcriptional, post-transcriptional
The difference between lncRNA and miRNA in the regulation of gene expression is that lncRNAs can regulate gene expression at both the __________ and ________ levels, while miRNAs regulate gene expression at the _________ level.
transcriptional and post-transcriptional, post-transcriptional
One of the major functions of a circRNA is to act as a _________.
miRNA sponge
