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Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data
Liliana Florea1,2, Lindsay Payer1,3, Corina Antonescu1
1McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States.
Frontiers in Molecular Biosciences
|September 27, 2021
Summary
We developed Alubaster software to detect Alu sequences in mRNA transcripts, revealing how these elements diversify the human transcriptome by creating new mRNA isoforms. This work enhances understanding of alternative splicing and gene expression.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Alu exonization diversifies the transcriptome, generating alternative mRNA isoforms.
- These events constitute approximately 5% of alternatively spliced exons in the human genome.
Purpose of the Study:
- To develop computational methods for detecting Alu sequence incorporation into mRNA transcripts.
- To build and characterize a collection of Alu-containing mRNAs from human brain samples.
Main Methods:
- Implementation of computational methods into Alubaster software.
- Analysis of large-scale RNA-seq data from 117 human frontal cortex samples (GTEx).
- Detection of Alu sequences from fixed, polymorphic, and rare/novel Alu elements.
Main Results:
- Characterization of Alu exonizations at 870 fixed Alu loci, with 237 novel events identified.
- Identification of hundreds of putative events involving polymorphic or rare Alu variants.
- Creation of a comprehensive resource of Alu-containing mRNAs and their expression patterns.
Conclusions:
- Alubaster software effectively detects Alu exonizations across diverse Alu element types.
- The characterized Alu-containing mRNAs provide insights into transcriptome diversification.
- This resource facilitates the study of tissue-specific expression and functional consequences of Alu incorporation.
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