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Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

Chromatin Structure and RNA Splicing

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Pre-mRNA Processing: Modification of pre-mRNA Ends

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...

Nonsense-mediated mRNA Decay

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Classification and Quantification of Unproductive Splicing Events.

L G Zavileyskiy¹, E A Chernyavskaya¹, M A Vlasenok¹

¹Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia.

|August 7, 2025

Summary

Nonsense-mediated decay (NMD) targets are identified using the new NMDj tool. NMDj precisely quantifies NMD-sensitive transcripts generated by alternative splicing events, improving gene expression understanding.

Keywords:

NMD nonsense mediated decay regulation splicing unproductive splicing

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Last Updated: Sep 12, 2025

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Area of Science:

Molecular Biology
Genetics
Bioinformatics

Background:

Eukaryotic cells utilize nonsense-mediated decay (NMD) to eliminate mRNAs with premature stop codons.
The interplay between NMD and alternative splicing (AS) generates NMD-sensitive transcripts (NMDTs), crucial for gene expression regulation through unproductive splicing.

Purpose of the Study:

To develop a novel computational tool, NMDj, for identifying, classifying, and quantifying NMDT-generating alternative splicing events.
To provide a method that overcomes limitations of existing tools by not relying on transcript partner matching.

Main Methods:

NMDj employs a unique approach using characteristic introns to distinguish NMDTs from other protein-coding transcripts.
The tool is designed for the accurate classification of complex AS events leading to NMDTs.

Main Results:

NMDj demonstrates superior precision in quantifying NMDT-generating AS events compared to existing methods, as validated on simulated RNA-Seq data.
The tool offers a generic and accurate method for classifying diverse AS events that produce NMDTs.

Conclusions:

NMDj provides a significant advancement in the accurate identification and quantification of NMDT-generating AS events.
This tool facilitates a deeper understanding of gene expression regulation through unproductive splicing mechanisms.