Abstract
The length of untranslated regions at the 3′ end of transcripts (3′UTRs) is regulated by alternate polyadenylation (APA). 3′UTRs contain regions that harbor binding motifs for regulatory molecules. However, the mechanisms that coordinate the 3′UTR length of specific groups of transcripts are not well-understood. We therefore developed a method, CSI-UTR, that models 3′UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals—CSIs). This approach facilitated (1) profiling of 3′UTR isoform expression changes and (2) statistical enrichment of putative regulatory motifs. CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes. Analysis of RNA-Seq datasets from neural tissue identified differential expression events within 3′UTRs not detected by standard gene-based differential expression analyses. Further, in many instances 3′UTR and CDS from the same gene were regulated differently. This modulation of motifs for RNA-interacting molecules with potential condition-dependent and tissue-specific RNA binding partners near the polyA signal and CSI junction may play a mechanistic role in the specificity of alternative polyadenylation.Source code, CSI BED files and example datasets are available at: https://github.com/UofLBioinformatics/CSI-UTR
Highlights
Detecting differential expression of regions of the 5′ and 3′ untranslated regions (UTRs) is of great importance for understanding the processes of transcription, translation, and transcript localization
Using polyA-Seq reads from the study by Derti et al (2012) (GEO series GSE30198; SRA accession SRP007359) which performed sequencing on a variety of tissues from human, mouse, and rat, we developed a pipeline for defining Cleavage Site Intervals (CSIs) in these species
Based on the methods outlined in the previous section, CSIs were constructed for the following genomes: human hg38, mouse mm10, and rat rn6
Summary
Detecting differential expression of regions of the 5′ and 3′ untranslated regions (UTRs) is of great importance for understanding the processes of transcription, translation, and transcript localization. The expansion of the known repertoire of UTRs improves the accuracy of alignment which is critically important for quantification of gene products using RNA-Seq. Beyond this, the study of these UTR splicing events represents an understudied but rich landscape for potential transcriptional regulation with broad implications for dynamic biological processes in many fields of research. The decreasing costs in sequencing, along with development of APA sequencing methods (polyA-Seq) (Fox-Walsh et al, 2011; Shepard et al, 2011; Derti et al, 2012) allow for a more thorough understanding of the complete transcript in (potentially) all its forms, including the 5′ and 3′ UTRs which play significant roles in both transcriptional and translational regulation
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