Long non-coding RNAs

Question 1

What does the % of non-coding DNA correlate with?

Answer 1

DNA compexity

Question 2

What is considered as a long non-coding RNA?

Answer 2

bigger than 200bp

Question 3

How are lncRNAs expressed?

Answer 3

In a more tissue/ cell-type specific manner than protein coding genes: they have fewer alternative splicing events

Question 4

Arrangements of lncRNA

Answer 4

1. Divergent
2. Sense
3. Intergenic
4. Antisense
5. Intronic

Question 5

Divergent lncRNA

Answer 5

lncRNA share the same promoter with the protein- coding gene but are transcribed in the opposite direction

Question 6

Sense lncRNA

Answer 6

the long non-coding transcription unit is inside the transcription unit of the protein-coding genes and the direction is the same

Question 7

Intergenic lncRNA

Answer 7

Long non-coding is located in the genomic space between 2 protein- coding genes

Question 8

Antisense lncRNA

Answer 8

long non-coding starts to be transcribed in the end of the protein- coding genes and this transcription gets in the opposite direction

Question 9

Intronic lncRNA

Answer 9

Non-coding RNAs whom transcription unit is inside one protein coding gene

Question 10

Ways lncRNA are expressed in the nucleus

Answer 10

1. Scaffold for complex formation
2. Controlled recruitment of TRs
3. Regulation of splicing
4. Regulation of chromosome looping
5. Formation and function of subnuclear structures

Question 11

Ways lncRNA are expressed in the cytoplasm

Answer 11

1. Control of translation rate
2. Control of mRNA decay
3. miRNA sequestration

Question 12

Control of translation rate

Answer 12

by binding to to mRNA in the cytoplasm they can activate/repress translation

Question 13

Control of mRNA decay

Answer 13

By recognising specific targets and recruiting/preventing the recruitment of nucleases of the target RNA

Question 14

miRNA sequestration

Answer 14

Can regulate other non-coding RNAs such as miRNA. When there is a high level of non-coding, the miRNA will bind to lncRNAs instead of mRNA and miRNA is inhibited: increased translation

Question 15

Controlled recruitment of TRs

Answer 15

lncRNAs can directly regulate recruitment of TRs

Question 16

Scaffold for complex formation

Answer 16

Many proteins recognise lncRNAs and may promote the formation of CRCs, regulating the reposition of histone modifications –> affecting gene expression

Question 17

Regulation of splicing

Answer 17

can interact with splicing factors and recruit splicing factors with particular locations on the mRNA

Question 18

Formation and function of subnuclear structures

Answer 18

lncRNAs can promote the formation of some nuclear structures

Question 19

Regulation of chromosome looping

Answer 19

Bridge promoters to enhancers to regulate the activation of gene expression

Question 20

lncRNA post-transcriptional modification

Answer 20

1. Adenosine N-6 methylation
2. Adenosine deamination to inosine
3. Uridine isomerisation to 5-ribosyluracil
4. 5- methylcytidine

Question 21

What can the post-transcriptional modifications cause?

Answer 21

Change the affinity of a protein that recognsies the RNA

Question 22

Effects of mutations in lncRNAs

Answer 22

1. eQTL: mutation in a region in lncRNAs causing the creation of a binding site of a transcription activator:- may cause expression of lncRNAs in tissues where it should not be expressed
2. Mutations causing exon skipping
3. Mutations in secondary structure

Question 23

What can lncRNAs be used for?

Answer 23

biomarker to perform diagnosis of the disease; works well as they have a restricted pattern of disease

Question 24

Enhancer eRNAs

Answer 24

cis-regulatory sequences that recruit transcription factors

Question 25

How do eRNAs work?

Answer 25

loop in proximity of the promoter and remodel its activity by promoting/repressing the recruitment of general transcription machinery

Question 26

Mechanisms of how eRNAs target gene expression?

Answer 26

1. Direct role in the control of the transcriptional role by building the lopp between the enhancer and the promoter
2. Mediate the interactions of TFs with cofactors
3. Deposition of histone marks
4. Facilitate RNA pol II transition to elongation