RNAi, miRNA, siRNA Pathways

• siRNA (small interfering RNA) is initially produced through the cleavage of short, double-stranded RNA.

Stem-Loop Formation

• ncRNAs (non-coding RNAs) require regions of complementary base-sequence to form stem-loop structures.

RNA Interference and Imperfect Complementarity

• In an experiment with C. elegans involving the injection of antisense and double-stranded RNAs similar but not identical to C. elegans mex-3, the mex-3 RNA is inhibited but not degraded.
• This results in the embryos from injected worms appearing green due to the miRNA pathway being activated instead of the siRNA pathway.
• miRNA is partially complementary to the mRNA, leading to inhibition rather than degradation.
• siRNA typically comes from viral infection or experimental treatments and has perfect complementarity to mRNA, leading to mRNA degradation.

Fire and Mello Conclusion

• Double-stranded RNA degrades more mex-3 mRNA than antisense RNA

Cas1 Mutation

• If the Cas1 protein is no longer produced due to a mutation, bacteria will lack adaptive immunity against secondary infections by bacteriophages.
• The CRISPR-Cas system defends bacteria against bacteriophages in three stages: adaptation, expression, and interference.
• Adaptation involves Cas1 and Cas2 proteins cutting bacteriophage DNA and inserting it into the CRISPR gene's spacer region.
• During the expression phase, CRISPR, tracr and Cas9 genes are expressed to produce the tracrRNA-crRNA-Cas9 complex.
• In the interference phase, the tracrRNA-crRNA-Cas9 complex targets and cleaves bacteriophage DNA.
• Without functional Cas1, the adaptation phase is impaired, preventing the bacteria from defending against the first infection and developing adaptive immunity.

Guide ncRNA

• MicroRNA (miRNA) functions as a guide ncRNA.

Mechanism Not Used for ncRNA Binding

• ncRNAs do not use stem loop structures to bind to specific DNA sequences.

Telomerase Function

• The protein component of telomerase functions to synthesize a DNA polymer using RNA as a template.

miRNA First Step

• Transcription from a nuclear gene is the initial step in the production of miRNA

COOLAIR

• COOLAIR regulates flowering in plants only after exposure to cold temperatures.

SRP Definition

• Proteins secreted from a cell are initially sorted to the appropriate locations (plasma membrane in prokaryotes, endoplasmic reticulum in eukaryotes) via the Signal Recognition Particle (SRP).

Stem-Loop Function

• An ncRNA consisting only of several stem-loop structures most likely functions by binding to components of the ribosome and facilitating its assembly.ncRNAs that interact with proteins usually have stem-loop structures whereas ncRNAs that bind to nucleic acid regions usually have single stranded regions for complementary base-pairing.

HOTAIR Mutation 2

• When the sequence in Region 2 of the HOTAIR ncRNA is mutated, it will likely bind to different target genes than the normal HOTAIR, but continue to inhibit their expression.
• HOTAIR has stem-loop structures that function as a scaffold for proteins that modify chromatin and guide these proteins to specific DNA targets via complementary base-pairing.

SRP Function

• An ncRNA called SRP-RNA facilitates the hydrolyzation of GTP, which is a necessary step in the release of SRP from a growing polypeptide at the endoplasmic reticulum.

RISC

• Complementary base pairing allows the miRNA or siRNA and the mRNA to interact.

HOTAIR ncRNA

• The ncRNA HOTAIR function as a scaffold and then a guide.

ncRNA Binding

• A short ncRNA with the sequence 5' AGCCCUAUGACGUU 3' is likely to bind to an mRNA that contains the sequence 3' GAUACUG 5'.
• ncRNAs use complementary base-pairing to bind to RNA and DNA molecules, and stem-loop structures for protein or small molecule binding.

SRP Function

• SRP RNA functions as a scaffold to target proteins to the ER lumen.

Modifying rRNAs

• An antisense RNA directs an enzyme to an rRNA sequence for covalent modifications of nucleotides in rRNAs.

miR-200

• The miR-200 class of miRNAs reduces tumor growth in terms of human health.

Ribozyme

• A ribozyme is the ncRNA that catalyzes an enzymatic reaction.

Mutation in CRISPR Gene

• A mutation in repeat 2 of the CRISPR gene will result in bacteria having adaptive immunity against the second infection with bacteriophage A, C and D, but not B.

HOTAIR Functions

• HOTAIR functions as a scaffold and as a guide.

Self-Splicing Intron

• The self splicing intron functions as a ribozyme.

TERC Function

• The RNA component of telomerase (TERC) functions as a template.