Non-coding/regulatory RNA

Question 1

MicroRNA discovery (profiling methods):

Answer 1

1) qRT-PCR 2) mRNA microarray 3) Nanostring 4) RNA-seq

Question 2

_________ of miRNAs frequent event in cancers

Answer 2

Downregulation

Question 3

52.5% located in areas of genome associated with development of cancer called _________

Answer 3

Cancer associated genomic regions (CAGR)

Question 4

SiRNAs as therapeutic targets challenges:

Answer 4

RNA half-life, delivery system, immune response and toxic effects, delivery to tumor, uptake by tumors, specific target recognition

Question 5

Primary structure RNA:

Answer 5

Sequence of nucleotides from 5’ end to 3’ end

Question 6

Secondary structure RNA:

Answer 6

Hydrogen bonds formed within molecule

Question 7

Tertiary structure RNA:

Answer 7

Locations of the atoms in 3D space

Question 8

RNAi

Answer 8

RNA interference

Question 9

RNA interference:

Answer 9

Silencing of gene expression by different types small RNAs (18-30 nt) piRNAs, siRNAs, miRNAs

Question 10

RNAi results in (4):

Answer 10

Translational inhibition, mRNA degradation, transcriptional silencing, chromatin remodeling

Question 11

small RNAs common features:

Answer 11

20-30 nt, associated with Argonatue (AGO) fam proteins

Question 12

AGO protein family subclades:

Answer 12

AGO, PIWI, WAGO

Question 13

PIWI subclade:

Answer 13

Associated with piRNAs, germ-cell specific

Question 14

AGO subclade:

Answer 14

miRNA, siRNA, piRNA, ubiquitously expressed

Question 15

Main biological role piRNAs:

Answer 15

Restrain spread of selfish genetic elements in germ cells, ex. transposons

Question 16

piRNA clusters correspond to _________

Answer 16

Transposon-rich regions

Question 17

piRNAs arise from __________

Answer 17

ssRNA precursors, independent of RNase III enzyme

Question 18

piRNAs biogenesis:

Answer 18

Primary piRNA processing pathway and amplification loop (Ping-pong cycle)

Question 19

siRNAs vs miRNAs

Answer 19

Both 18-25 nt, siRNA silencing target deg, miRNA silencing translational inhibition or deg

Question 20

siRNAs induce _________ and ________

Answer 20

mRNA cleavage (Dicer, RISC-AGO) and chromatin remodeling (RITS, Chp1)

Question 21

miRNA characteristics:

Answer 21

Processed from long endogenous ssRNA, RISC containing AGO protein, guides binding of RISC to 3’UTR of target mRNA leading to post-transcrip silencing

Question 22

miRNA location:

Answer 22

Intronic majority, more than 50% transcribed polycistronic, primary transcript molecules (pri-miRNAs) fold into imperfect dsRNA-like hairpins

Question 23

pri-miRNA structure

Answer 23

Basal segments->lower stem(11 bp)->cleavage by Drosha->upper stem (22 bp)->cleavage by Dicer->terminal loop

Question 24

Drosha (pri-miRNA Step 1)

Answer 24

RNAse III endonuclease found in nucleus, functions in combo with DGCR8, generates 65 bp product with 3’ overhang

Question 25

DGCR8

Answer 25

Double stranded RNA binding protein

Question 26

Exportin and Ran-GTP role (pri-miRNA Step 2)

Answer 26

Export pri-miRNAs to cytoplasm

Question 27

Dicer (pri-miRNA Step 3)

Answer 27

RNase III-like endonuclease, works in complex with TRBP, final 22 bp miRNA duplex with 3’ overhang

Question 28

TRBP

Answer 28

dsRNA binding protein

Question 29

let-7 role

Answer 29

Regulates Dicer expression in negative feedback loop

Question 30

RISC (pri-mRNA Step 4)

Answer 30

miRNA duplex incorporated into microRNA ribonucleoprotein complex, mature miRNAs one strand selected for function

Question 31

Main function of AGO subclade:

Answer 31

Expose and present miRNAs to target RNA

Question 32

Non-canonical pathway miRNA

Answer 32

Mirtron (short introns that after transcription are made into miRNA mimics)

Question 33

miRNA-mRNA interactions in animals

Answer 33

miRNA pair imperfectly with mRNA targets, usually in 3’UTR, induce translational repression

Question 34

miRNA-mRNA interactions in plants

Answer 34

miRNAs base pair near perfect complementarity to mRNA targets, trigger endonucleolytic cleavage of mRNA similar to siRNAs

Question 35

miRNA-mRNA silencing mechanisms (post-transcriptional)

Answer 35

1) Translational repression (5’ cap binding or elongation block) 2) mRNA turnover (shortening of polyA tail or removal of 5’ cap and deg) 3) endonucleolytic cleavage

Question 36

miRNAs in vertebrates

Answer 36

Abundant and highly conserved, repress gene expression, tissue specific expression (zebrafish), cell proliferation and differentiation

Question 37

IsomiRs/Sequence heterogeneity

Answer 37

miRNA sequences that have variations with respect to the reference sequence