Regulatory RNAs

Question 1

why is imperfect basepairing in miRNAs important?

Answer 1

1. Allows them to have many targets

2. Binding of Ago

Question 2

ago-clip

Answer 2

miRNA/mRNA chimeras isolated, sequenced to determine better seed sequence and rules for basepairing/targeting

Question 3

How do miRNAs cause decay?

Answer 3

1. Translation/elongation
2. Deadenylation
3. Degradation

Question 4

How do siRNAs cause decay?

Answer 4

perfect basepairing and endonucleolytic cleavage followed by decay

Question 5

T/F. Drosophila has two pathways for RNAi, humans have 4

Answer 5

True

Question 6

circular RNAs

Answer 6

made by backsplicing, can be important for miRNA function - by acting as miRNA sponge or RBP sponge - can use to endogenously regulate RNA function

Question 7

piRNAs

Answer 7

typically longer the si/miRNAs, in nucleus and involved with guarding genome from transposition events (downregulate transcription from repetitive seqs)

Question 8

what are three examples of mechanisms of regulatory RNAs?

Answer 8

block protein binding, change RNA structure, tether protein

Question 9

tmRNA

Answer 9

bacteria, transfer-messenger RNA, has tRNA nubbin and an ORF, allows for ribosome rescue on non-stop cleaved mRNAs

Question 10

rhyB example

Answer 10

regulatory rhyB RNA binds targets under low iron conditions and causes decreased ribosome binding, as well as targeted mRNA cleavage

Question 11

vitamin B12 example

Answer 11

riboswitch - binds metabolite, causing conformation change and freeing of effector domain which regulates downstream events

Question 12

enzymatic RNA example

Answer 12

hammerhead, a self-cleaving endo-nucleolytic RNA

Question 13

characteristics of miRNAs (4)

Answer 13

1. encoded as gene (pol II typically)
2. Fold into hairpin structure
3. Well conserved
4. Many potential targets / imperfect pairing important

Question 14

pri-miRNAs

Answer 14

primary micro RNAs, capped and polyadenylated precursors that are processed by Drosha in nucleus and Dicer in the cytoplasm

Question 15

what do miRNAs look like?

Answer 15

20+ bp duplex with 2 nt 3’ overhangs

Question 16

important domain for Dicer/Drosha

Answer 16

PAZ, binds 3’ end of RNA and acts as ruler to set length

Question 17

T/F. siRNAs are produced by mammalian cells

Answer 17

False, they are exogenously introduced

Question 18

how are duplex RNAs sorted on Argonaute

Answer 18

asymmetric loading, weaker base pairing at 5/ end of duplex, cleavage and release of passenger strand

Question 19

how does the loading of miRNAs vs siRNAs affect their activity?

Answer 19

miRNAs imperfect binding leads to no conformational change and translational repression/decay. Binding of siRNAs to perfectly complementary targets leads to cleavage at a precise position

Question 20

how to miRNAs ID targets

Answer 20

by using seed pairing, although imperfect base pairing leads to challenges in miRNA target ID

Question 21

how can circular RNAs affect gene regulation?

Answer 21

by acting as sponges for miRNA or RBPs

Question 22

hcRNAs

Answer 22

heterochromatic RNAs, maintain integrity of centromeres, involved in histone silencing

Question 23

evolutionary origins of regulatory RNAs

Answer 23

ancestral role in defense response against genomic parasites such as transposons