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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...

Alternative RNA Splicing

Alternative RNA Splicing

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

Chromatin Structure and RNA Splicing

Chromatin Structure and RNA Splicing

Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...

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Related Experiment Video

Updated: Dec 17, 2025

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

Epigenome-based splicing prediction using a recurrent neural network.

Donghoon Lee^1,2, Jing Zhang^1,2, Jason Liu^1,2

¹Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.

Plos Computational Biology

|June 26, 2020

Summary

This summary is machine-generated.

Alternative RNA splicing, crucial for transcriptome diversity, is increasingly linked to transcription. This study reveals how chromatin context, changing during transcription, influences splicing decisions, impacting gene expression.

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Last Updated: Dec 17, 2025

Using the E1A Minigene Tool to Study mRNA Splicing Changes

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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells

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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

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Published on: September 15, 2021

Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Alternative RNA splicing expands transcriptome diversity in metazoans.
Splicing is now understood to occur concurrently with transcription (co-transcriptional splicing).
Emerging evidence suggests physical proximity between the spliceosome and RNA Polymerase II (Pol II).

Purpose of the Study:

To investigate the influence of epigenetic context on co-transcriptional splicing.
To develop a model predicting exon inclusion based on dynamic chromatin changes during transcription.
To understand the spatio-temporal features of epigenetic signals in splicing regulation.

Main Methods:

Surveyed epigenetic signatures around splice sites.
Developed a recurrent neural network (RNN) model to predict exon inclusion.
Analyzed the model's weights to identify key determinants of splicing outcomes.

Main Results:

Epigenetic signatures around splice sites exhibit asymmetric profiles.
Splicing factors are not always enriched at exon junctions.
Spatio-temporal features of chromatin context, alongside DNA sequence, are critical for predicting exon inclusion (achieving >80% precision-recall).

Conclusions:

The dynamic, asymmetric nature of chromatin context during transcription significantly impacts co-transcriptional splicing.
Interpretable models can elucidate the physical layout of splicing regulation.
Epigenetic modifications play a crucial role in directing alternative splicing events.