AUTHOR=Florea Liliana , Payer Lindsay , Antonescu Corina , Yang Guangyu , Burns Kathleen 

TITLE=Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=8

YEAR=2021

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2021.727537

DOI=10.3389/fmolb.2021.727537

ISSN=2296-889X

ABSTRACT=<p><italic>Alu</italic> exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of <italic>Alu</italic> sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects <italic>Alu</italic> sequences derived from both fixed and polymorphic <italic>Alu</italic> elements, including <italic>Alu</italic> insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of <italic>Alu</italic>-containing mRNAs. In particular, we detected and characterized <italic>Alu</italic> exonizations occurring at 870 fixed <italic>Alu</italic> loci, of which 237 were novel, as well as hundreds of putative events involving <italic>Alu</italic> elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of <italic>Alu</italic>-containing mRNAs and their tissue-specific expression patterns.</p>