Long non coding RNAs

Question 1

What were the ideas for what “junk DNA”?

Answer 1

Chromosomal pairing, genome integrity, gene regulation, mRNA processing, reservoir for evolutionary innovation.

Question 2

What is the transcriptome?

Answer 2

Set of all RNA transcripts

Question 3

What is translatome?

Answer 3

mRNA fragments that are being translated.

Question 4

What is ribosome profiling (Ribo-seq)?

Answer 4

A method based on deep sequencing of ribosome-protected mRNA fragments. Compares ribosome-bound mRNAs, which are undergoing active translation, with total mRNA pool in the cell.

Question 5

What did Ribo-seq experiments show about stem cells?

Answer 5

The majority of lnc RNAs are translated into small peptides.

Question 6

What is the take home message for studying gene expression?

Answer 6

It is a dynamic expression it is important to remember that it is a dynamic and messy landscape where rules and regulations are constantly changed and adapted.

Question 7

What are lncRNAs?

Answer 7

represent a class of transcribed RNA molecules that are longer than 200 nucleotides. Not translated into proteins but might translate into polypeptides.

Question 8

Why are they important?

Answer 8

Recent discoveries increasingly indicate only 7% of disease associated single nucleotide polymorphisms SNPs are located in the protein- coding regions. Rest located in gene regulatory regions or in intergenic regions.

Question 9

What are stand alone lnc-RNAs?

Answer 9

Distinct transcription units with no overlap with protein coding genes.

Question 10

What are natural antisense transcripts?

Answer 10

Transcription that is opposite the sense DNA strand of annotated transcription units.

Question 11

What are pseudogenes?

Answer 11

Genes that have lost their coding potential due to mutations (2-20% can still be transcribed).

Question 12

What are long intronic ncRNAs?

Answer 12

Large-scale transcripts encoded within the introns of annoted genes. Some regions are spliced, become lncRNAs and then splice the same gene itself.

Question 13

What are promoter/enhancer associated transcripts?

Answer 13

Produced from vicinity of start sites in both directions. When DNA unwinds for transcription it opens up structure to recognition from random transcription so required to regulate this.

Question 14

What is the mechanism of action?

Answer 14

Recruits tethers and scaffolds. (used in epigenetic regulation). decoys, regulators and Pol II inhibitors (direct effect on transcription, regulating TF. Can also interfere with pol activity).

Question 15

What is trans mechanism of action?

Answer 15

Controls transcription of genes on other chromosomes.

Question 16

What is cis mechanism of action?

Answer 16

Controls transcription of genes on same chromosome.

Question 17

What do nuclear compartments do?

Answer 17

Contribute to formation/stability/structure of nuclear bodies that perform localised functions within the nucleus.

Question 18

How is transcription regulated?

Answer 18

Process of transcription of a lnc-RNA that is regulatory, rather than the transcript itself.

Question 19

How is miRNA blocked and act as pseudo targets?

Answer 19

Masking binding sites for miRNAs in specific regions of 3’UTRs or acting as sponges for them.

Question 20

What is MALAT1?

Answer 20

A druggable lncRNA for targeted anti-cancer approaches.

Question 21

Where do lncRNAs localize too?

Answer 21

The nucleus. Generally less expressed than protein coding genes. While displaying tissue- specific expression patterns.

Question 22

What makes them novel master regulators?

Answer 22

Respond to a wide variety of tumours and hematological malignancies. Evidence supports aberrant patterns of expression in lncRNAs in cancer.

Question 23

What is an interactor of MALAT1?

Answer 23

TAR DNA binding protein TDP43 located in the mouse brain. Predominantly nuclear protein that regulates transcription, alternative splicing and RNA stability. Have been associated with fronto temporal dementia.

Question 24

How is MALAT1 transcribed?

Answer 24

By RNA polymerase II from the human chromosome 11q13. Its biogenesis relies on the tRNA processing machinery.

Question 25

What can MALAT1 be affected by?

Answer 25

TFs, epigenetics, miRNAs, binding proteins such as METTL16.

Question 26

What is evidence for MALAT1’s role in cancer?

Answer 26

Correlates with tumour size, advanced tumour stage.

Question 27

What are strategies to halt MALAT1’s oncogenic activity?

Answer 27

ASOs antagonize. Independence on RISC machinery, higher specificity and fewer off targets. siRNAs several studies support successful knockdown.

Question 28

How do sncRNAs work?

Answer 28

Serve as specificity factors directly bound effector proteins to target nuclei acid molecules via base pairing interactions.

Question 29

Give examples of sncRNAs?

Answer 29

siRNAs, miRNAs, (both argonaute proteins) piRNAs piwi not much known.

Question 30

What are transposons?

Answer 30

DNA sequences that are able to move from one location to another in the genome. Can promote gene inactivation, modulate gene expression, or induce illegitimate recombination. Used as an evolutionary variability factor but constantly trying to suppress them.

Question 31

What do siRNAs consist of?

Answer 31

Guide strand assembles into RISC complex. Passenger strand ejected and degraded.

Question 32

How do endogenous-siRNAs arise?

Answer 32

From structures loci that can pair intramolecularly to produce long dsRNA, complementary overlapping transcripts and bi-directionally transcribed loci.

Question 33

How are siRNAs used to experimentally knockdown gene expression?

Answer 33

Gene specific RNA degradation can be obtained with RNA interference (RNAi) technology. siRNA effectively silences endogenous gene expression in a sequence-specific manner. Relatively simple to generate.