What is no go decay?
Introduction. The No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stalled ribosomes1,2. NGD occurs when translation elongation is blocked by the presence of stable intramolecular or intermolecular RNA structures, enzymatic cleavage, chemically damaged sequences or rare codons1,3,4,5,6,7,8.
What is nonstop mediated decay?
Non-stop decay (NSD) is a cellular mechanism of mRNA surveillance to detect mRNA molecules lacking a stop codon and prevent these mRNAs from translation.
What is mRNA degradation?
mRNA degradation is an important mechanism for controlling gene expression in bacterial cells. This process involves the orderly action of a battery of cellular endonucleases and exonucleases, some universal and others present only in certain species.
What is an exon exon junction?
An exon junction complex (EJC) is a protein complex which forms on a pre-messenger RNA strand at the junction of two exons which have been joined together during RNA splicing. The EJC has major influences on translation, surveillance and localization of the spliced mRNA.
Where does nonsense-mediated decay occur?
One of the best-studied RNA surveillance pathways is the Nonsense-mediated decay (NMD) pathway, which targets mRNAs harboring premature termination codons (PTC) for degradation. This mechanism operates in the cytoplasm and is intimately linked to translation termination (2,3).
What is the function of tmRNA?
Transfer-messenger RNA (tmRNA) is a bifunctional RNA that has properties of a tRNA and an mRNA. tmRNA uses these two functions to release ribosomes stalled during translation and target the nascent polypeptides for degradation.
Why does RNA get degraded?
There are two main reasons for RNA degradation during RNA analysis. First, RNA by its very structure is inherently weaker than DNA. RNA is made up of ribose units, which have a highly reactive hydroxyl group on C2 that takes part in RNA-mediated enzymatic events. This makes RNA more chemically labile than DNA.
Why does mRNA need to be degraded?
While cells degrade messenger RNA to regulate the amount of proteins that can be translated from each mRNA molecule, they also modify mRNA molecules in a way that increases the stability of the molecule and increases the protein output under specific conditions and at certain times.
Why is mRNA degraded after translation?
What are intron spanning primers?
Primers of intron spanning primer pairs are located at both sides of an intron and will therefore generate a larger product on genomic DNA (containing the intron).
What are splice junctions?
Splice-junction sequence signals are strongly conserved structural components of eukaryotic genes. These sequences border exon/intron junctions and aid in the process of removing introns by the RNA splicing machinery.
Why is nonsense-mediated decay important?
Nonsense-mediated RNA decay (NMD) is an essential RNA quality control and gene regulatory mechanism that is conserved among eukaryotes [1,2,3,4,5,6,7,8,9]. NMD safeguards the quality of the transcriptome and maintains cellular homeostasis by eliminating transcripts that harbor premature termination codons (PTCs).
What is required for nonsense-mediated decay?
At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation.
Where is tmRNA found?
bacteria
The tmRNA-SmpB system is found in bacteria and some organelles and has not yet been identified in archaea or in eukaryotes targeted to the cytoplasm. Aside from one report of a bacterium with a frameshift mutation in smpB, it has generally been considered that all bacteria have the system.
What is the function of the Shine-Dalgarno sequence?
This ribosomal binding site in bacterial messenger RNA became known as the Shine-Dalgarno (SD) sequence. It enables initiation of protein synthesis by aligning the ribosome with the start codon.
What happens after degradation of mRNA?
After export to the cytoplasm, mRNA is protected from degradation by a 5′ cap structure and a 3′ poly adenine tail. In the deadenylation dependent mRNA decay pathway, the polyA tail is gradually shortened by exonucleases.
What causes mRNA decay?
The role of P-bodies in mRNA quality control One important aspect of P-body’s protein composition is the presence of enzymes, which promote mRNA decay, including the deadenylase CCR4 (Sheth and Parker, 2003; Andrei et al, 2005) and the DCP1–DCP2 decapping complex (Ingelfinger et al, 2002; Sheth and Parker, 2003).
What does exon spanning mean?
“Span Exon Junction” implies the presence of reads with one end mapping to one exon, and the other end mapping to another exon, thus spanning the intermediate intron.
How do you know if primers are intron spanning?
This is how I do it: First with Primer-Blast find out what is the mRNA reference sequence, then open the reference sequence, and with the Pick Primer function (using Primer3 and BLAST) you can detect the location of the primer and if it is crossing an exon-exon junction.