Types of RNA

Question 1

What is transcribed?

Answer 1

Estimation of 70-90% of genome transcribed.

Question 2

What does evidence for function consist of?

Answer 2

Expression levels that are very high, high degree of conservation, experimental evidence that ncRNA is required for biological process.

Question 3

At steady state what is the most common RNA?

Answer 3

Ribosomal RNA

Question 4

What is the percentage of each RNA in mass?

Answer 4

80-90% rRNA, 10-15% tRNA, 3-7% mRNA

Question 5

What is the most to least common type of RNA by number of molecules?

Answer 5

tRNA, rRNA, mRNA

Question 6

What is the function of mRNA?

Answer 6

To carry genetic information from DNA in the nucleus to the ribosomes in the cytoplasm, where it serves as a template for protein synthesis.

Question 7

What is the function of rRNA?

Answer 7

Ribosomal, form basic structure of ribosome. Catalyze protein synthesis.

Question 8

What is the function of tRNA?

Answer 8

Transfer. Adaptors between mRNA and amino acids.

Question 9

What is the snRNAs?

Answer 9

Small nuclear, variety of nuclear processes, including splicing.

Question 10

What is the snoRNAs?

Answer 10

Small nucleolar. Processing and chemical modifications of RNAs in nucleus of eukaryotic cells.

Question 11

What are miRNAs?

Answer 11

micro. Regulate gene expression by preventing translation of mRNAs.

Question 12

What is siRNAs?

Answer 12

Small interfering. Direct degradation of selective mRNAs.

Question 13

What are piRNAs?

Answer 13

Piwi-interacting. Bind to piwi proteins and protect from transposable elements.

Question 14

What are lncRNAs?

Answer 14

Long noncoding. Regulate diverse cell processes.

Question 15

What can ribozyme do?

Answer 15

Catalyse peptide bond formation.

Question 16

Where is RNA in ribosome?

Answer 16

Main component of catalytic centre with proteins residing in the periphery.

Question 17

What are ribosomes made from?

Answer 17

Catalytic complexes made from more than 50 different proteins and several RNA molecules.

Question 18

How long are tRNA molecules?

Answer 18

80 nucleotides and can fold into precise 3D structures.

Question 19

What is an example of DNA giving rise to multiple different mRNA transcripts in splicing?

Answer 19

Striated muscle mRNA, smooth muscle mRNA, fibroblast mRNA, fibroblast mRNA, brain mRNA.

Question 20

What is post translational cleavage of RNA transcripts for?

Answer 20

To release specific fragments which can then function independently. RNA fragmentation significantly expands the already extraordinary spectrum of transcripts present within eukaryotic cells.

Question 21

How does the genome represent the palimpsest?

Answer 21

Arranged in an interleaved, overlapping fashion in both DNA and RNA. An ancient parchment on which the original text has been overwritten. So a single locus can produce multiple transcripts that use shared sequences.

Question 22

What does RNA sequencing do?

Answer 22

Provide data for all the transcripts expressed in a particular sample. Coupled with high throughput sequencing. Quantitative. Highly technical and relatively expensive. Rely on computational statistical analysis.

Question 23

What are 6 applications of RNA sequencing?

Answer 23

Abundance estimation (no. transcripts sequenced). Alternative splicing. RNA editing. Finding novel transcripts. Ribo-seq. Single cell sequencing.

Question 24

What is ribo-seq?

Answer 24

Analysis of those RNAs in active translation: ribosome profiling.

Question 25

What are the steps to RNA sequencing?

Answer 25

RNA capture, cDNA preparation, adaptor ligation, DNA sequencing, read alignment, read counts.

Question 26

How is RNA sequencing done?

Answer 26

Start with isolation of a sample of RNA. Convert it to cDNA. Sequence it on a high throughput platform to generate tens of millions of short reads. Reads are aligned to an existing gene framework. Counts per gene determined.

Question 27

What does RNA sequencing suggest about degradation process?

Answer 27

There is a highly regulated and precise processing of RNAs.

Question 28

What are the different ways of mapping the reads from sequencing to the genome?

Answer 28

If something is transcribed equally and fully to genome fragments will appear randomly. If a specific region is preferentially kept then this will show up at one point on the genome.

Question 29

What are the different parts of mature tRNA for?

Answer 29

D-loop and TΨC loop: Endonucleolytic cleavage and exonuclease digestion.

Question 30

What is the 1-tRF series and how is it produced?

Answer 30

A class of tRNA derived fragments. Produced by RNase Z (or ELAC2) cleavage of pre-tRNA during tRNA processing.

Question 31

What are tRFs?

Answer 31

tRNA derived fragments. generated from the 5’ end of mature tRNA molecules, specifically from the region spanning the 5’ leader sequence (the portion of the tRNA that is just upstream of the mature tRNA sequence).

Question 32

What does ANG do?

Answer 32

Cleaves the mature tRNA in the anticodon loop to produce 5’-tiRNA and 3’-tiRNA. These are used in stress response and cell survival in stress response.

Question 33

How is the 5’-tRF series derived?

Answer 33

5’-end of mature tRNAs by endonucleolytic cleavage and exonuclease digestion in the D-loop.

Question 34

How is the 3’- tRF series produced?

Answer 34

Cleavage in the T-loop results in production of 3’-tRF series.

Question 35

What are multifaceted functions of tRNA-derived small tRNAs in human cancer cell line?

Answer 35

Inhibit translation by forming a stress granule with translation initiation factors. tsRNAs with terminal oligo-G motifs form an RNA G-quadruplex structure.

Question 36

What are multifaceted functions of tRNA-derived small tRNAs in human stem cells?

Answer 36

Short tsRNAs show different binding affinities with initiation factors based on modifications at C8 position (U to C). C8 tRNAs inhibit translation but U8 tsRNAs don’t.

Question 37

What are multifaceted functions of tRNA-derived small tRNAs in thedrasophila cell line?

Answer 37

tsRNAs recognize target mRNAs through conserved 7-mer complementary sequence matches and inhibit target mRNA translation in an AGO-dependent manner.

Question 38

What are multifaceted functions of tRNA-derived small tRNAs in human cancer cell line for ribosome biogenesis?

Answer 38

30tsRNA-LeuCAG binds to mRNA unfolding duplexed RNA structure which increases the translation of RPS18/15 protein. Increased ribosome biogenesis and translation.

Question 39

What are multifaceted functions of tRNA-derived small tRNAs in human cancer cell line for archaea?

Answer 39

tsRNA-Val competes with 16S rRNA of small ribosomal subunit 30S interfering with mRNA loading.

Question 40

What are circular RNAs (Circ RNAs)?

Answer 40

Covalently closed, endogenous biomolecules in eukaryotes with tissue specific and cell specific expression patterns.

Question 41

What do circ RNAs do?

Answer 41

Abundant and evolutionarily conserved. Act as microRNA or protein inhibitors. (sponges). Have been implicated in diseases like diabetes, neurological disorders, cardiovacular, cancer.

Question 42

Where are circRNAs derived from?

Answer 42

Canonical splice sites and their biogenesis is dependent on canonical splicing machinery.

Question 43

What are the functions of circRNA?

Answer 43

Not much known but crosslinking immunoprecipitation data suggests they interact with RBPs to act as RNA and protein sponges. Scaffold to mediate complex formation of enzymes and substrates. Subset can undergo cap-independent translation under specific conditions although most are non-coding.