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Developmental Genetics and Embryonal Cancers > lncRNAs > Flashcards

lncRNAs Flashcards

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1
Q

how long is the Xist transcript

A

17kb spliced polyadenylated transcript

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2
Q

How many genes have an antisense RNa

A

approximately 20%

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3
Q

Nme some genes that have antisense RNAs

A

WT1 and n-myc however antisense RNAs dont control their protein levels

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4
Q

What is Msx1

A

It is muscle like homeobox 1

It has an antisense RNA and the msx-1 levels are regulated by antisense trasncripts

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5
Q

Which part of msx1 does the antiense strand overlap

A

exon 2

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6
Q

What do the different isoforms of cerbA do

A

isorform 1) encodes the thyroid hormone receptor

isoform 2) inhbits 3 action

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7
Q

What does the antisense of c-erbA do

A

It inhibits splicing and therefore leads to regulation of the protein isofrom balance

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8
Q

What is the sense transcript of SCA8 and what is thought tot be involved in

A

KLHL1 –> thought to be involved in the cytoskeleton organisation in brain cells

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9
Q

What is the defect in spinocerebellar ataxia

A

Expansion of the CUG repeat in SCA8 –> may interfere with splicing or sequester TF

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10
Q

sWhat are pseudogenes

A

Defective copies of genomes (mutated ORF) that have accumulated during evolition
approximately 20000 in the human genome

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11
Q

Give an example of a pseudogene positively reuglated experssion of the normal gene

A

The makorin-p1 pseudogene positively regulated makrin short form gene possibly as the pseudogene may instead attract regulators to degrade it or the transcriptional suppressors may instead suppress the pseudogene

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12
Q

Give an example of negative regulation by a pseudogene

A

An antisense trasncript in a pseudogene of the neural nitric oxide synthase protein may suppress it

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13
Q

Describe how HBA2 is silenced by LUC7 in alpha thalassaemia

A

LUC7L is downsteam of HBA2 and the transcript is read in the opposite direction
In alpha-thalassaemia the polyA signal for LUC7L is delted
Hence you get read throguh transcription of LUC7L which extends downsteadm of the HBA2 locus
this leads to hypermethylation of the HBA2 promoter causing epigenetic silencing

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14
Q

Give some example of imprinted genes with anti-sense RNAs

A

AIr
KCNG1Ot1
Xist

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15
Q

What happens with deletion of ICE/AIR

A

Get bi-allelic transcription of IGF2

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16
Q

What allele is air transcribed from

A

Air is transcribed from PATERNAL ALLELES ONLY –> leads to silencing of igf2 and slc genes
In maternal alleles methylation of ICE turns of Air and the Igf2r and Slc genes are transcribed

17
Q

What is Tsix

A

It is an antisense transcript of Xist which if present can block Xist function and lead to X activation

18
Q

How might Tsix work

A

Prevents binding of factors needed to stabilist Xist
Prevents efficient transcription of the Xist gene
May bind to the putative blocking factors somwehere in teh Xist 3’ region
Enables the bidning of develpmentally regulated factors to the Xic region

19
Q

What lncRNA in cancer increases metastatic breaset cancer

A

HOTAIR

20
Q

How does HOTAIR increases the risk of breast cancer metastasisng

A

Complexes with PRC2 and causes it to get new targets and shuts down lots of genes

21
Q

What are microsatellite repeats

A

They are short repeats (2-6bp) polymorphic repeat squences

22
Q

What is the repeat expansion in myotonic dystropgy 1

A

CUG repeat expansion in the 3’ UTR of the DMPK

23
Q

What is the repeat expansion in myotonic dystrophy 2

A

CCUG repeat expanision in the ZNF intron 9

24
Q

What are the characteristics of lncRNAs

A

200nt- 100kb, lack an ORF
RNA Pol II Transcribes them
Generally lower expression than coding genes

25
Q

Give an example of some imprinted lncRNAs

A

H19

Xist

26
Q

What 2 lncRNAs have roles in metastasis

A

HOTAIR

MALAT1

27
Q

What is MALAT1

A

Metastasis Associated Lung Adenocarcinoma Transcript
Higher levels in cancers and poor prognsosis
Transcript processes to produce a short tRNA and a MALAT1 transcript
Implicated in cell mobility –> inhibiting reduced the invasive potential of cervical cancer cells

28
Q

What lncRNA can stimulate p53

A

MEG3 –> often high level in brain and pituitary but undetectable in brain cancer

29
Q

What is HULC

A

a miRNA that is highly upregulated in liver cancer –> acts as a sponge to miRNA 372

30
Q

What is ANRIL and how does it fucntion

A

Antinsense noncldoing RNA in the INK4 locus

ANRIL can mediate silencing of the INK4b-ARF-INK4a locus by recruiting PRC1/2

Developmental Genetics and Embryonal Cancers (18 decks)

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