Small non-coding RNAs 1 & 2 Flashcards
As a rule of thumb, what differs between lncRNAs and small non-coding RNAs, functionally?
Long non-coding RNA works as buffers for miRNA and RBPs, they can also affect chromatin remodeling.
Small non-coding RNA primarily affects transcription and translation.
How are small non-coding RNAs important for the RNAi machinery? Briefly explain RNAi.
The RNAi consists of
1. AGO1/2 protein
2. TRBF protein
3. DICER protein.
4. small dsRNA –> ssRNA
Process
1. There are three categories of small non-coding RNAs that interact w/ RNAi; miRNAs, siRNAs, and piRNAs. Separate questions for their processing.
- TRBF and dicer load small dsRNA to AGO1/2, the RNA is then denatured into being single-stranded.
- ssRNA guides the RISC complex to where it’s complementary.
In cancer, small non-coding RNAs can be proto-onco genes ____ TSGs.
and
What’s the characteristics and functions of small nucleolar RNA (snoRNAs)?
Characteristics
1. snoRNAs are 80-120 bp long.
2. Present in nucleoli and cajal bodies. (Nucleoli are present in the nucleus, and known for the biogenesis of ribosomes. Cajal bodies are membrane-less intranuclear organelles. Known for histone mRNA processing).
3. Contains exons and introns.
Functions
1. Guides tRNAs and rRNAs.
2. Guides RNA modifications.
3. Modifies uridine to pseudo-uridine.
What are tRNA-derived fragments (tRFs)?
Characteristics
1. 15-40 nt long.
2. Expression is 1% of normal tRNAs.
Functions
1. Regulates the cellular stress response.
2. Facilitates differentiation of stem cells –> mRNA instability, reduced translation and growth inhibition.
How are miRNA, siRNA and piRNA differentially processed before interacting with the RNAi machinery?
miRNA genetic sequence is referred to as pri-pre-miRNA. It gets transcribed into a hairpin dsRNA which is referred to as pre-miRNA. The hairpin gets processed by drosha intracellularly (gets shortened) then by dicer cytosolically (hairpin bend gets removed).
siRNA can derive from various dsRNA fragments of from outside the cell. They get processed by dicer.
piRNA are associated to particular AGO proteins referred to as PIWI-proteins. piRNA derive from cluster-like genetic regions, much like the CRISPR regions. The maturation is independent from drosha and dicer and can mediate DNA and histone methylations specifically to transposon sites (which have opposite effects).
What are the consequences of RNAi with 1. miRNA 2. siRNA 3. piRNA?
miRNA –> mRNA cleavage
siRNA –> Translational repression
piRNA –> mRNA degradation
miRNA ____ be uridylated when entering the RISC complex, but it needs to be before being activated.
can’t
What are p-bodies (processing bodies)?
P-bodies are distinct phase shifts in the cytosol. They contain lots of degraded and soon-to-be degraded mRNAs. Some mRNAs can exit p-bodies and reinitiate translation, which leads us to believe its secondary function is mRNA storage.
Dicer is a holoenzyme, which enzymatic components are present?
2x RNAse 2
1x dsRNA binding domain
1x helicase domain
1x PAZ domain (PIWI argonaute Zwille, which binds 3’ of miRNAs).
What’s the difference between mono- and polycistronic miRNAs?
monocistronic miRNA : if a locus only contains this one miRNA, it is monocistronic.
polycistronic miRNA : if a locus contains multiple miRNAs, they are polycistronic.
(fact: miRNAs often bind the 3’ UTR of miRNA w/ small seed regions)
A: How many AGO proteins are there in humans?
B: What domains are present in AGO proteins?
A: 8
B:
1. PAZ domain (PIWI argonaute zwille)
2. MID domain
3. PIWI domain (P-element associated with wimpy testes)
What’s the function of ribonucleoproteins (small RNPs)?
Interacts with
1. rRNA
2. snRNA
3. telomeres
The ribosome contains __RNA, they are referred to as _1, _2, _4 and _5.
sn, U
