Lec5miRNAsAndOtherNoncodingRNAs Flashcards
what is TERC
RNA in telomerase
RNA THAT TELOMERASE uses, it is the template
What is mRNA
mature RNA gets translated into protein
what is rRNA
ribosomal RNA, makes the large and small subunit of the ribosome and function in translation
What is SnRNA
Small nuclear RNA, functions in splicing
What is SnoRNA
Small nucleOlar, function in chemically modifying rRNA
What is TERC
RNA added to telomerase
What is XIST
X chromosome inactivation, has binding sites for histone methylase
what is the function of microRNA
multiple imp roles in gene regulation, notably in development and implicated in same cancers
what is the function of Piwi binding RNA
derived from repeats; expressed only in germ line cells, where they limit excess transposon activity
what is the function of endogenous short interfering RNA
derived from pseudogenes, inverted repeats, involved in gene regulation in Somatic cells and may be involved in same types of transposon
What is the RNA interference (RNAi) pathway?
Pathway for destroying long ds RNAs from viruses or transposable elements
In the RNA interference (RNAi) pathway, what chops us the ds DNA?
dicer
Dicer chops up ds DNA and makes what? (RNAi)
22bp(ds) segments called siRNA
where are the siRNA going to go? and do?(RNAi)
go to argonaute
argonaute has a helicase component and it will separate the two strands in (siRNA)
What happens to the single fragments after argonaute? (RNAi)
One will be left behind and the other will be incorporated in the complex guide
The guide complex can go into two pathways:
RISC and RITS
The guide complex can go into two pathways: explain the RICS pathway (RNAi)
Use the guide RNA to look for its complementary sequence and endonuculease activity to chop it up
EXCAT W/C BP
The guide complex can go into two pathways: explain the RITS pathway (RNAi)
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
RNAi is a natural pathway; the pathway is also used for what besides ENDO siRNA
exogenous siRNA
What does dicer work with and recognize?
Dicer works with transposons and inverted repeats; dicer recognizes dsRNA
What does dicer produce?
siRNAs of about 22bps with overhangs
T/F dicer does not have sequence specificity for cleavage
TRUE
what produces produces single stranded RNA that can lead to W/C base pairing on RNAs for degradation (RISC) or for transcriptional silencing (RITS)
endonuclease Argonaute
what is argonaute?
Argonaute is an endonuclease that generates a 20 nucleotide gRNA strand
What is dicer?
Dicer: Divides long DS DNA (entire rotavirus genome)
**DS endonuclease*
What is argonaute
Argonaute: Helicase + Endonuclease
What is RISC?
RISC(RNA Interference silencing complex): Cleaves and degrades
What is RITs
RITS (RNA Interference transcriptional silencing): Stops transcription
What is guide strand
guide strand: Strand that will w/c base pair with target strand
What is the passenger strand
passenger strand: Released by argonaute complex
What are microRNAs?
MiRNA will ultimately W+C bp with mRNAs to INHIBIT TRANSLATION
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.
What is the key feature of miRNA?
hair pin due to intramolecular bp and a cap
What is the hair pin caused by (miRNA)
hair pin due to intramolecular bp
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
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
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
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
What does miRNA interact with to stop translation
block 3UT
miRNA can be transcribed from what?
INTRONIC REGIONS
miRNA can prevent what?
miRNA can prevent premature gene translation (important in embryonic development)
If miRNA pairs extensively, what happens?
rapid mRNA degradation with Argonaute cleavage
If miRNA base pairs less extensively , what happens?
translational repression and eventually mRNA degradation (3UT region)
miRNA does not have what pathway?
RITS
Where of miRNA primary transcripts originate from?
Encoded by themselves or in introns protein coding genes (Via RNA polymerase 2)
what is this?
miRNA
Piwi RNA are the same as what? what is the one exception
Same as RISC Complex but in specialized cell (Germ cells)
What does piRNAs regulate?
piRNAs regulate transposition (inhibit transposition)
what do we target? (piwi)
Targets the RNAs coming off the pi transposons (represent sequences by viruses over millions of years)
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
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
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
piRNAs can be involved in both?
piRNAs can be involved both in transposon degradation and transposon transcriptional silencing
Without piwi proteins what happens?
Without piwi proteins, germ cells have large amounts of transposon transcription.
What presence of what defines germ cell stem cells
DDX4
what is one of the piwi proteins ?
One of the piwi proteins is an RNA helicase, termed ddx4.
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)
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
Total RNA binding domain count for exam:
SR (splicing enhancement, alternative splicing)
Dead box (RNA helicase)
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
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
What are examples of PIWI family proteins?
MILI, MIWI2
MILI and MIWI2 produce what
they produce piRNAs
Mice without mili and miwi2 have?
Mice without MILI and MIWI2 expressed retrotransposons and had MVH deficiencies
____=DDx4 in mice
MVH
If you lack MVH in mice they have what?
infertility issues
From a stem cell, we can get what?
oocyte
