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Lec5miRNAsAndOtherNoncodingRNAs Flashcards

1
Q

what is TERC

A

RNA in telomerase

RNA THAT TELOMERASE uses, it is the template

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2
Q

What is mRNA

A

mature RNA gets translated into protein

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3
Q

what is rRNA

A

ribosomal RNA, makes the large and small subunit of the ribosome and function in translation

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4
Q

What is SnRNA

A

Small nuclear RNA, functions in splicing

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5
Q

What is SnoRNA

A

Small nucleOlar, function in chemically modifying rRNA

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6
Q

What is TERC

A

RNA added to telomerase

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7
Q

What is XIST

A

X chromosome inactivation, has binding sites for histone methylase

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8
Q

what is the function of microRNA

A

multiple imp roles in gene regulation, notably in development and implicated in same cancers

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9
Q

what is the function of Piwi binding RNA

A

derived from repeats; expressed only in germ line cells, where they limit excess transposon activity

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10
Q

what is the function of endogenous short interfering RNA

A

derived from pseudogenes, inverted repeats, involved in gene regulation in Somatic cells and may be involved in same types of transposon

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11
Q

What is the RNA interference (RNAi) pathway?

A

Pathway for destroying long ds RNAs from viruses or transposable elements

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12
Q

In the RNA interference (RNAi) pathway, what chops us the ds DNA?

A

dicer

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13
Q

Dicer chops up ds DNA and makes what? (RNAi)

A

22bp(ds) segments called siRNA

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14
Q

where are the siRNA going to go? and do?(RNAi)

A

go to argonaute

argonaute has a helicase component and it will separate the two strands in (siRNA)

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15
Q

What happens to the single fragments after argonaute? (RNAi)

A

One will be left behind and the other will be incorporated in the complex guide

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16
Q

The guide complex can go into two pathways:

A

RISC and RITS

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17
Q

The guide complex can go into two pathways: explain the RICS pathway (RNAi)

A

Use the guide RNA to look for its complementary sequence and endonuculease activity to chop it up

EXCAT W/C BP

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18
Q

The guide complex can go into two pathways: explain the RITS pathway (RNAi)

A

Transcriptional Silencing

  • If there was a release of one of the guide RNA’s next to the 5’ end of a newly synthesized RNA (we just started synthesis so CURRENTLY being synthesized) we are going to use the RITS complex. We can then bring in a histone methylates to close chromatin and stop transcription

** basically shutting down the virus

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19
Q

RNAi is a natural pathway; the pathway is also used for what besides ENDO siRNA

A

exogenous siRNA

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20
Q

What does dicer work with and recognize?

A

Dicer works with transposons and inverted repeats; dicer recognizes dsRNA

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21
Q

What does dicer produce?

A

siRNAs of about 22bps with overhangs

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22
Q

T/F dicer does not have sequence specificity for cleavage

A

TRUE

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23
Q

what produces produces single stranded RNA that can lead to W/C base pairing on RNAs for degradation (RISC) or for transcriptional silencing (RITS)

A

endonuclease Argonaute

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24
Q

what is argonaute?

A

Argonaute is an endonuclease that generates a 20 nucleotide gRNA strand

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25
What is dicer?
Dicer: Divides long DS DNA (entire rotavirus genome) **DS endonuclease*
26
What is argonaute
Argonaute: Helicase + Endonuclease
27
What is RISC?
RISC(RNA Interference silencing complex): Cleaves and degrades
28
What is RITs
RITS (RNA Interference transcriptional silencing): Stops transcription
29
What is guide strand
guide strand: Strand that will w/c base pair with target strand
30
What is the passenger strand
passenger strand: Released by argonaute complex
31
What are microRNAs?
MiRNA will ultimately W+C bp with mRNAs to INHIBIT TRANSLATION
32
Can miRNAs W-C base pair with some mismatching or need perfect pairing?,
miRNAs can W-C base pair with some mismatching, which basically means one miRNA can regulate multiple mRNAs. basically means one miRNA can regulate multiple mRNAs.
33
What is the key feature of miRNA?
hair pin due to intramolecular bp and a cap
34
What is the hair pin caused by (miRNA)
hair pin due to intramolecular bp
35
If the ds has a cap, when do you add the cap?
when you modifying the primary transcript and can only be added when RNA pol 2 is phosphorylated
36
miRNA are produced by what and how can we tell?
miRNAs have a cap and poly A tail on c terminal domain which then gets lost in the nucleus Which tells us that they are produced by RNA POLYMERASE 2
37
Same as endo, what happens to break down the ds (miRNA)
dicer comes in then argonaute will break down the ds and produce the guide strand to go down a pathway
38
What are the two pathways for miRNA
imperfect match--> block 3 UT (untranslated region)= does not allow for ribosome assembly so no TRANSLATION perfect march-->RICS pathway
39
What does miRNA interact with to stop translation
block 3UT
40
miRNA can be transcribed from what?
INTRONIC REGIONS
41
miRNA can prevent what?
miRNA can prevent premature gene translation (important in embryonic development)
42
If miRNA pairs extensively, what happens?
rapid mRNA degradation with Argonaute cleavage
43
If miRNA base pairs less extensively , what happens?
translational repression and eventually mRNA degradation (3UT region)
44
miRNA does not have what pathway?
RITS
45
Where of miRNA primary transcripts originate from?
Encoded by themselves or in introns protein coding genes (Via RNA polymerase 2)
46
what is this?
miRNA
47
Piwi RNA are the same as what? what is the one exception
Same as RISC Complex but in specialized cell (Germ cells)
48
What does piRNAs regulate?
piRNAs regulate transposition (inhibit transposition)
49
what do we target? (piwi)
Targets the RNAs coming off the pi transposons (represent sequences by viruses over millions of years)
50
piRNA can be be involved in what?
piRNAs can be involved in both transposon degradation and transposon transcriptional silencing. WE CAN DESTROY THE RNAS WITH THE ENDONUCLEASE AND GUIDE RNAS LIKE RISC AND WE CAN SUCH DOWN TRANSCRIPTION WITH RECRUITEMENT OF CHROMATIN MODIFYING PROTEINS (HISTONE METHYLASE) LIKE RITS
51
what happens if the vestigial transposon complex is allowed to go on?
If this vestigial transposon complex is allowed to go on and DS RNA accumulate then the germ cells are destroyed, and we will not produce gametes
52
T/F: piRNAs have a high relevance in gametogenesis; infertility results if piRNA proteins are not degraded
False: piRNAs have a high relevance in gametogenesis; infertility results if piRNA proteins are NOT degraded
53
piRNAs can be involved in both?
piRNAs can be involved both in transposon degradation and transposon transcriptional silencing
54
Without piwi proteins what happens?
Without piwi proteins, germ cells have large amounts of transposon transcription.
55
What presence of what defines germ cell stem cells
DDX4
56
what is one of the piwi proteins ?
One of the piwi proteins is an RNA helicase, termed ddx4.
57
DDx4 is what?
The ddx4 protein was identified as being expressed in ADULT female ovaries infertility treatments. RNA helicase and marker for stem cells to develop egg cells Represents a family of proteins with a conserved domain, the dead box domain (section of polypeptide)
58
what is the mouse equivalent of ddx4?
mouse vasa homolog (mvh) and its human equivalent, ddx4 Hope is to address infertility issues with these stem cells
59
Total RNA binding domain count for exam:
SR (splicing enhancement, alternative splicing) Dead box (RNA helicase)
60
Another important list: effects of nonconding RNAs
RNA degradation: EXACT MATCH Inhibition of translation: MiRNA Gene/transcription silencing: PiRNA miRNA inhibit Translation, Endo siRNA (RITS) inhibit transcription
61
PiRNA and ddx4
PIWI family proteins: MILI, MIWI2 : they produce piRNAs Mice without MILI and MIWI2 expressed retrotransposons and had MVH deficiencies MVH=DDx4 in mice=RNA Helicase VASA= V in MVH= essential for germ cell development MVH may play some roles in piRNA production therefore DNA methylation of retrotransposons
62
What are examples of PIWI family proteins?
MILI, MIWI2
63
MILI and MIWI2 produce what
they produce piRNAs
64
Mice without mili and miwi2 have?
Mice without MILI and MIWI2 expressed retrotransposons and had MVH deficiencies
65
____=DDx4 in mice
MVH
66
If you lack MVH in mice they have what?
infertility issues
67
From a stem cell, we can get what?
oocyte

Genetics (12 decks)

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