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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...

Alternative RNA Splicing

Alternative 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...

RNA Splicing

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Pre-mRNA Processing: RNA Splicing

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Protein Complexes with Interchangeable Parts

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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

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Using the E1A Minigene Tool to Study mRNA Splicing Changes

Using the E1A Minigene Tool to Study mRNA Splicing Changes

Published on: April 22, 2021

Alternative Splicing May Not Be the Key to Proteome Complexity.

Michael L Tress¹, Federico Abascal², Alfonso Valencia³

¹Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain.

Trends in Biochemical Sciences

|October 8, 2016

Summary

Most human genes produce a single main protein, despite thousands of detected alternative transcripts. Proteomics data suggest most alternative splicing events may not yield functional proteins, challenging protein diversity assumptions.

Keywords:

RNA-seq alternative splicing dominant isoforms functional isoforms homology proteomics

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Area of Science:

Molecular Biology
Proteomics
Genomics

Background:

Alternative splicing is widely considered a primary driver of protein diversity.
RNA sequencing (RNA-seq) studies detect numerous alternatively spliced transcripts.
However, mass spectrometry-based proteomics has not consistently identified these diverse isoforms.

Purpose of the Study:

To investigate the discrepancy between detected alternative transcripts and identified protein isoforms.
To determine the extent to which alternative splicing contributes to functional protein diversity.
To assess the biological plausibility and evolutionary conservation of identified alternative protein isoforms.

Main Methods:

Large-scale mass spectrometry-based proteomics analysis.
Comparison of identified protein isoforms with annotated alternative transcripts from RNA-seq data.
Analysis of cross-species conservation and functional domain integrity for alternative isoforms.

Main Results:

Proteomics reliably identifies only a small fraction of annotated alternative splicing isoforms.
Most human genes predominantly produce a single main protein isoform.
Identified alternative isoforms often exhibit high cross-species conservation and preserve functional domains, suggesting biological relevance.
A significant proportion of alternative exons appear to lack selective pressure.

Conclusions:

The contribution of alternative splicing to protein diversity may be overestimated.
A large majority of predicted alternative transcripts might not be translated into functional proteins.
Proteomics data indicate that functional protein isoforms are generally conserved and biologically plausible.