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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

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

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...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: 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...

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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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Published on: December 9, 2016

RCDA: a highly sensitive and specific alternatively spliced transcript assembly tool featuring upstream consecutive

Xiaolu H Sturgeon¹, Katheleen J Gardiner

¹Department of Pediatrics, Linda Crnic Institute for Down Syndrome, University of Colorado Denver, Mail Stop 8608, 12700 E. 19th Avenue, Aurora, CO 80045, USA. Xiaolu.sturgeon@colorado.edu

|September 14, 2012

Summary

Researchers developed RCDA, a novel genome-based transcript assembly tool. This efficient method accurately reconstructs mRNA sequences and reduces splice variant numbers, improving transcriptomic analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Current mRNA sequence assembly tools face challenges with long run times and excessive splice variant generation.
Complex transcript datasets require more efficient and accurate assembly methods.

Purpose of the Study:

To introduce RCDA, a genome-based transcript assembly tool designed for efficiency and accuracy.
To overcome limitations of existing automated transcript assembly methods.

Main Methods:

RCDA utilizes a two-component system: RCluster for recursive transcript clustering and DAssemble for composite transcript generation via directed acyclic graph path-finding.
Exon structures are validated using upstream consecutive exon patterns and depth-first-search path retention.
Biologically reasonable filters were applied.

Main Results:

RCDA processed over 23,000 transcripts from human chromosome 21 in approximately 4 hours.
The tool demonstrated superior performance compared to ECgene in reconstructing RefSeq transcripts.
RCDA effectively limited the total number of transcripts and transcripts per gene.

Conclusions:

RCDA offers a computationally efficient and accurate solution for genome-based transcript assembly.
The tool's methodology ensures that assembled transcripts are supported by experimental data.
RCDA represents a significant advancement in analyzing complex transcriptomic data.