Non-coding lncRNAs 2

Question 1

What is the main known function of a growing number of lncRNAs?

Answer 1

Gene regulation

Question 2

lncRNA transcription can affect genes on the same chromosome …

Answer 2

while the actual lncRNA molecule has no effect

Question 3

How can lncRNA effect neighbouring genes?

Answer 3

Increase accessibility of DNA regulatory elements (e.g. enhancers) in chromatin

Block neighbouring gene expression (transcriptional interference)

Question 4

What mediates transcript dependent modes of lncRNA gene regulation?

Answer 4

The RNA molecule produced

Question 5

What are the functions of nuclear lncRNA transcripts?

Answer 5

Act at site of expression + distant location in nucleus

Question 6

What are the functions of cytoplasmic lncRNAs?

Answer 6

Function post-transcriptionally

Question 7

Name an example of lncRNAs that accumulate at their site of synthesis + act in cis in the nucleus

Answer 7

H19 (gene imprinting)
EMICERI (dev. of drug resistance in melanoma)
PVT1 regulation of c-MYC oncogene (multiple cancers)

Question 8

Name an example of lncRNAs that move away from site of synthesis + act in trans (regulate genes on other chromosomes)

Answer 8

HOTAIR (breast cancer metastasis)

Paupar (neuroblastoma)

Question 9

Name the 3 basic mechanisms of actions of transcript dependent lncRNA gene regulation

Answer 9

Scaffold
= acts as platform which other molecular components can assemble

Decoy
= Bind to target molecules to titrate them away

Guide
= Guide regulatory complexes to their site of action

Question 10

Name an example of a lncRNA that acts as a scaffold

Answer 10

HOTAIR lncRNA co-ordinately binds PRC2 + LSD1 in the nucleus
-> targets them to sites on chromatin

Question 11

Name an example of a nuclear lncRNA that acts as a decoy

Answer 11

PANDA binds + sequesters NF-YA transcription factor in the nucleus

Question 12

How do guide lncRNAs recognise + bind to genomic binding sites?

Answer 12

Directly
= base pair w/ complementary DNA in a sequence specific manner -> forms RNA-DNA-DNA triplex

= through specific lncRNA-RNA interactions at transcribed genes

Indirectly
= via association w/ a transcription factor

Question 13

How can cytoplasmic lncRNAs regulate gene expression post-transcriptionally?

Answer 13

Regulating mRNA stability

Modulating levels of mRNA translation

Competing for the binding of shared microRNAs (decoy)

Question 14

Name an example of lncRNA that acts as a guide + forms a lncRNA-DNA-DNA triplex in cancer cells

Answer 14

MIR100HG binds to p27 (CDK1B) gene promoter + silences it

• > proliferation of triple-negative breast cancer (TNBC) cells
• > low survival

Question 15

Name an example of cytoplasmic lncRNA that acts as a decoy

Answer 15

PTENP1 = PTEN pseudogene
Similar to PTEN tumour suppressor gene

PTENP1 = rich in cytoplasm

• > PTENP1 completes w/ PTEN mRNA for binding to miRNAs
• > PTEN is not down regulated by miRNAs

PTENP1 = often deleted in melanoma

Question 16

What are the 2 possible ways to interfere w/ function of cancer causing lncRNA oncogenes?

Answer 16

Silencing lncRNA expression

Disruption of lncRNA function

Question 17

How do you silence lncRNA expression?

Answer 17

Transcript degradation
= by siRNAs (in cytoplasm)
-> 19-22 nts long
-> associate w/ RNA-induced silencing complex (RISC)
-> guided to target lncRNA
-> Ago2 cleaves lncRNA

= by anti-sense oligonucleotides (ASOs) (in nucleus)

• > 12-25 nts long
• > bind to lncRNA (base pairing)
• > recruits RNase H1 which cleaves lncRNA

Question 18

What are the 2 advantages of nucleic acid based drugs as cancer therapies?

Answer 18

Selectively target any unique region of human transcriptome

Provide ability to target the “undraggable” portions of genome

Question 19

What are the 2 problems of nucleic acid based drugs as cancer therapies?

Answer 19

Delivery
= how to get molecules to right location of the body

Designing oligonucleotides w/ minimal to no off-target effects or toxicity

Question 20

How do you disrupt lncRNA function?

Answer 20

Use anti-sense oligonucleotides (ASOs) or small molecules to block lncRNA interaction w/ miRNA