RNA Decay and Degradation Mechanisms

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Questions and Answers

What is one of the primary functions of siRNAs in cells?

Blocking synthesis of disease-causing proteins (correct)

Enhancing mRNA stability

Increasing ribosomal activity

Promoting gene expression

What is a key difference between siRNAs and miRNAs regarding their origins?

siRNAs are derived from longer RNA products while miRNAs are internally sourced (correct)

Both originate from extracellular sources

miRNAs are derived from longer RNA products while siRNAs originate from miRNAs

Both are derived from short RNA products

Which enzyme is involved in the processing of pre-siRNA into mature siRNA?

Dicer (correct)

Drosha

Ago

RNA polymerase

How does the siRISC complex contribute to genome integrity?

By directing heterochromatin formation Signup and view all the answers

Which factor is NOT essential in improving siRNA gene-silencing efficiency?

Incorporating miRNA seed sequences Signup and view all the answers

What is typically a characteristic of long non-coding RNAs (lncRNAs) in mammalian cells?

They are longer and can assist in gene silencing processes Signup and view all the answers

What is the consequence of using minimal siRNA concentrations in experiments?

Reduces the likelihood of unintended sequence cutting Signup and view all the answers

Why does siRNA require high complementarity with its target mRNA?

To ensure specific targeting and degradation Signup and view all the answers

What enzyme is primarily responsible for degrading mRNA from the 5' end after the cap is removed?

XRN1 Signup and view all the answers

Which complex is involved in the 3' to 5' decay of mRNA?

Exosome Signup and view all the answers

In deadenylation-independent mRNA decay, what is the role of the protein Edc3?

To bind to the decay-inducing regulatory element Signup and view all the answers

What feature characterizes deadenylation-independent mRNAs?

They can be degraded without losing their polyA tail. Signup and view all the answers

How do endonucleases contribute to mRNA decay?

They generate unprotected ends by cleaving mRNA. Signup and view all the answers

Which statement about RNA interference is true?

MicroRNAs are approximately 21-25 nucleotides long. Signup and view all the answers

After the decapping process in deadenylation-independent decay, which enzyme begins the degradation of mRNA?

XRN1 Signup and view all the answers

What happens to the polyA tail during deadenylation-independent decay?

It is protected from degradation. Signup and view all the answers

What is the primary function of Box C/D snoRNAs?

To add methyl groups to RNA Signup and view all the answers

Which type of snoRNA modifies RNA by changing it into pseudouridine?

Box H/ACA snoRNA Signup and view all the answers

What do orphan snoRNAs lack that distinguishes them from other types?

Identified functions or targets Signup and view all the answers

How do snoRNAs ensure modifications are made to the correct locations on RNA?

Using a lock and key mechanism Signup and view all the answers

What role do snoRNPs play in the function of snoRNAs?

They facilitate snoRNA binding to pre-RNA Signup and view all the answers

How can snoRNAs be linked to diseases?

By being dysregulated in certain conditions Signup and view all the answers

What is the primary function of riboswitches in bacteria?

To regulate gene expression without proteins. Signup and view all the answers

What function does scaRNA perform?

It assists in RNA splicing via snRNP production Signup and view all the answers

Where are riboswitches typically located within bacterial mRNAs?

In the 5' untranslated region (5' UTR). Signup and view all the answers

What is one of the evolutionary roles of some snoRNAs?

To act as a source for small regulatory RNAs Signup and view all the answers

How do riboswitches affect gene expression when a metabolite concentration is low?

They promote transcription initiation. Signup and view all the answers

What happens to a riboswitch when the concentration of its metabolite reaches a high level?

It undergoes a shape change that terminates transcription. Signup and view all the answers

How do translational riboswitches control gene expression?

By affecting the accessibility of the ribosome binding site. Signup and view all the answers

What role do aptamers play in gene expression regulation?

They can change shape upon binding a ligand. Signup and view all the answers

Which type of riboswitch can create structures that stop transcription?

Transcription-regulating riboswitches. Signup and view all the answers

What can some aptamers do in response to binding with a ligand?

Act as their own enzymes. Signup and view all the answers

What is the primary difference in stability between prokaryotic and eukaryotic mRNAs?

Prokaryotic mRNAs exist in high concentrations, while eukaryotic mRNAs are fleeting. Signup and view all the answers

Which process allows the cell to control protein synthesis without breaking down mRNA?

Translational silencing Signup and view all the answers

What is a key factor that determines the stability of mRNA within the cell?

The cap and polyA tail structure Signup and view all the answers

What causes mRNA to be marked for degradation?

Shortening of the polyA tail Signup and view all the answers

Which pathway is most commonly responsible for the decay of mRNAs?

Deadenylation-dependent mRNA decay Signup and view all the answers

What role does the CCR4 protein play in mRNA degradation?

It helps remove the polyA tail. Signup and view all the answers

Which direction can mRNA be degraded after the removal of its polyA tail?

Both 5' to 3' and 3' to 5' Signup and view all the answers

Which complex is involved in the decapping of mRNA during the 5' to 3' decay process?

DCP1–DCP2 complex Signup and view all the answers

Study Notes

RNA Decay/Degradation

mRNA degradation controls how long mRNA can be used to make proteins, which controls the abundance of a particular protein.
The life of an mRNA is determined by a combination of translational silencing and degradation.
Translational silencing refers to the control of protein synthesis from mRNA without breaking it down.
Degradation pathways control mRNA stability through the removal of the 5' cap and/or the 3' polyA tail.

Degradation Machinery

The degradation machinery targets mRNAs that lack a polyA tail, marking them for degradation.
mRNA degradation can occur in two directions: 5' to 3' and 3' to 5'.

Deadenylation-Dependent mRNA Decay

Most mRNAs are degraded through this pathway.
Deadenylation occurs when enzymes called deadenylases shorten the polyA tail, making the mRNA susceptible to degradation.
The CCR4 mechanism is a common way for mRNA degradation through the removal of the polyA tail.

Additional Steps in Deadenylation-Dependent mRNA Decay

Fast degradation can occur when certain proteins target the mRNA for expedited destruction.
The Lsm1–7 complex attaches to the 5' end of the mRNA, promoting cap removal (decapping) via the DCP1-DCP2 complex.
XRN1, a 5'-3' exoribonuclease, degrades the mRNA from the 5' end once the cap is removed.
The exosome is a multi-protein complex that degrades mRNA from the 3' end.
DcpS removes the cap from the 5' end after the exosome has acted upon the mRNA, effectively completing the decay process.

Deadenylation-Independent mRNA Decay

Certain mRNAs are degraded via this pathway without first losing their polyA tail, making them deadenylation-independent.
In instances where the polyA tail is protected, the cell recruits decapping machinery.
Edc3, an enhancer of decapping-3, assists in this process by binding to decay-inducing regulatory elements, signaling for the decapping machinery to initiate.
The DCP1/DCP2 complex removes the 5' cap, and subsequent degradation is then performed by XRN1.

Endonuclease-Mediated mRNA Decay

Endonucleases cleave mRNAs into two fragments, each with an unprotected end, leaving them vulnerable to XRN1 and the exosome.
This pathway is arguably the most efficient method for mRNA degradation.
Endonucleases target specific mRNAs, providing precise control over mRNA levels.

RNA Interference

RNA interference is a gene regulation system that uses small RNA molecules such as microRNA (miRNA) and small interfering RNA (siRNA).

MicroRNA (miRNA)

miRNA is small, single-stranded RNA, typically 21-25 nucleotides long.
miRNAs target mRNA molecules based on sequence complementarity, downregulating gene expression.
miRNAs have the potential to block the synthesis of disease-causing proteins.

Small Interfering RNA (siRNA)

siRNA is a highly specific form of small RNA.
siRNAs play a role in genome integrity protection and responding to foreign nucleic acids, like viruses.
In plants, the siRISC directs heterochromatin formation by associating with nascent RNA and RNA polymerases, leading to methylation of DNA by DMT, resulting in inactive, tightly packed DNA (heterochromatin).
In mammals, a similar process occurs with long non-coding RNAs (lncRNAs).

siRNA Synthesis

siRNA begins as a long dsRNA.
Drosha cleaves the strand, creating hairpin structures (pre-siRNA fragments).
Dicer further cleaves these fragments, removing the hairpin.
Ago binds to the mature siRNA, forming a RISC complex.
The guide strand is selected, while the other strand is discarded, leaving a single-stranded siRNA.
The guide strand directs the RISC to a perfectly complementary RNA target, which is then degraded.

siRNA vs. miRNA

siRNA
- Externally sourced
- Derived from longer RNA products
- Requires high complementarity (specific targeting)
- More likely to cleave mRNA
miRNA
- Internally sourced
- Shorter RNA products
- Requires a 6-8 nucleotide "seed" for complementarity (broad targeting)
- More likely to repress translation
Both siRNA and miRNA use Drosha, Dicer, and Ago in their respective pathways.
Both miRNAs and siRNAs can be synthesized as ~21 nucleotide RNA duplexes for inducing mRNA silencing.

Improving Gene-Silencing Efficiency with siRNA

Longer dsRNA, while potent, activates the immune system, so using smaller, processed siRNAs is preferred.
Targeting specific mRNA regions enhances silencing, as certain regions are more effective targets.
Guide strand accuracy is critical to avoid silencing incorrect sequences.
Using minimal siRNA concentrations prevents off-target effects.
Avoiding miRNA-like effects by skipping miRNA seed sequences in siRNA design.
Multiple siRNAs targeting the same mRNA increase the likelihood of effective silencing.

Small Nucleolar RNAs (snoRNAs)

snoRNAs are small RNA molecules that modify other RNA molecules.
They play crucial roles in ribosome biogenesis.

snoRNA Types

Box C/D snoRNAs are involved in methylating RNA, adding stabilizing tags.
Box H/ACA snoRNAs catalyze the conversion of certain uridine bases in RNA into pseudouridine, maintaining RNA structure and function.
"Orphan" snoRNAs lack clearly defined functions, with unknown targets and purposes.
snoRNAs guide two primary modifications in other RNA molecules:
- Methylation: Box C/D snoRNAs add a methyl group to the 2’O ribose portion of RNA.
- Pseudouridylation: Box H/ACA snoRNAs convert certain RNA bases into pseudouridine.
snoRNAs temporarily bind to specific sites in pre-rRNA or pre-tRNA, ensuring modifications occur at the correct locations.
snoRNAs collaborate with snoRNPs, small nucleolar ribonucleoproteins, to form complexes that enable precise RNA modifications.

Other snoRNA Functions

Some snoRNAs facilitate alternative splicing, resulting in shorter RNA versions that can generate different protein forms from the same gene.
Some snoRNAs contribute to the formation of small regulatory RNAs, which can resemble snoRNAs across species.
snoRNAs can potentially attach to AGO2, hinting at a role in gene regulation.
Dysregulation of snoRNAs has been linked to various diseases, making them promising biomarkers for diagnosis and monitoring.

Small Cajal Body-Specific RNAs (scaRNAs)

scaRNAs are a type of snoRNA found within the Cajal body in the cell nucleus.
scaRNAs assist in the production of snRNPs, essential for RNA splicing.
scaRNAs guide methylation and pseudouridylation of specific snRNAs (U1, U2, U4, U5, and U12).
scaRNAs ensure that snRNPs are appropriately modified, enhancing RNA splicing efficiency.

Riboswitches

Riboswitches are RNA sequences in bacteria that regulate gene expression independently of proteins, acting as an alternative to traditional transcriptional regulation.
They are located in the 5' untranslated region (5' UTR) of bacterial mRNAs.
They are cis-acting elements, influencing the same RNA molecule they are part of.
They bind small molecules like metabolites or metal ions, which act as ligands.
Binding of these ligands induces structural changes in the mRNA.

Riboswitch Types

Translational riboswitches control gene expression by affecting ribosome binding site or start codon accessibility, influencing protein synthesis.
Transcription-regulating riboswitches can create structures that stop transcription by destabilizing the RNA, preventing RNA polymerase from functioning properly.

Aptamers

Aptamers are unique RNA molecules capable of folding into specific shapes that allow them to bind to other molecules selectively, similar to proteins and antibodies.
When aptamers bind to ligands, they undergo conformational changes, which can affect gene expression, typically by reducing protein production.
Aptamers can also contribute to mRNA degradation, alter end processing, or function as enzymes in response to ligand binding.

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Description

This quiz explores the intricate mechanisms of mRNA decay and degradation, including translational silencing and the pathways that determine mRNA stability. It covers the roles of the degradation machinery and the impact of deadenylation on mRNA lifespans. Test your understanding of the processes that control protein synthesis.