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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...

RNA Splicing

RNA Splicing

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

Alternative RNA Splicing

Alternative RNA Splicing

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...

Protein Networks

Protein Networks

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CoSpliceNet: a framework for co-splicing network inference from transcriptomics data.

Delasa Aghamirzaie¹, Eva Collakova², Song Li^3,4

¹Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, 24061, USA. delasa@vt.edu.

|October 30, 2016

Summary

This summary is machine-generated.

Alternative splicing enhances transcript and protein diversity, impacting molecular function. A new tool, CoSpliceNet, infers co-splicing networks to identify splicing regulators and RNA-binding motifs.

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Area of Science:

Molecular Biology
Genetics
Bioinformatics

Background:

Alternative splicing is crucial for eukaryotic transcript and protein diversity.
Understanding splicing factor interactions is key to deciphering this post-transcriptional process.
The extent of alternative splicing's role in molecular function diversification remains unclear.

Purpose of the Study:

To assess transcript and protein diversity generated by alternative splicing.
To develop a method for inferring co-splicing networks.
To identify splicing regulators and RNA-binding motifs.

Main Methods:

Comparison of transcript and protein attributes between splice variants and isoforms.
Development of CoSpliceNet, integrating co-expression and motif discovery.
Application of CoSpliceNet to RNA sequencing data.

Main Results:

Alternative splicing increases transcript and protein diversity in Arabidopsis embryos.
CoSpliceNet identified candidate splicing regulators and RNA-binding motifs.
An unexpected role for the unfolded protein response in embryo development was revealed.

Conclusions:

The presented methods can assess transcript diversity and protein plasticity in any biological system.
Candidate regulators, targets, and RNA-binding motifs for splicing factors can be predicted.
CoSpliceNet is available for broader research applications.