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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

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Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

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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...

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Related Experiment Video

Updated: Jan 2, 2026

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

Characterizing the interplay between gene nucleotide composition bias and splicing.

Sébastien Lemaire¹, Nicolas Fontrodona¹, Fabien Aubé¹

¹Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d'Italie Site Jacques Monod, F-69007, Lyon, France.

|December 1, 2019

Summary

Genome nucleotide composition bias influences exon recognition during splicing. Specific splicing factors bind GC-rich or AT-rich exons, linking genome organization to alternative splicing regulation.

Keywords:

Chromatin organization Genomic Nucleotide composition bias Splicing

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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

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Published on: April 26, 2017

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Nucleotide composition bias significantly impacts human genome organization in 1D and 3D.
Investigating the relationship between nucleotide composition bias and alternative splicing regulation is crucial.

Purpose of the Study:

To explore the interplay between nucleotide composition bias and the regulation of exon recognition in splicing.
To identify specific splicing factors associated with GC-rich and AT-rich exons.

Main Methods:

Analysis of multiple RNA-sequencing datasets.
Identification and characterization of splicing factors.
Assessment of RNA secondary structures and binding sites.
Correlation analysis with chromatin organization and genomic domains.

Main Results:

Two distinct groups of splicing factors were identified, targeting approximately 3200 GC-rich and 4000 AT-rich exons.
GC-rich exons exhibit RNA secondary structures and depend on U1 snRNP proteins.
AT-rich exons feature decoy branch points and depend on U2 snRNP proteins.
Nucleotide composition bias affects local chromatin organization and exon recognition.

Conclusions:

Regional nucleotide bias leaves a footprint at the exon level, influencing splicing constraints.
Local chromatin organization and specific splicing factor recruitment alleviate these constraints.
Nucleotide composition bias directly links genome organization to alternative splicing.