Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs.

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

SUBMITTER: Harrison BJ 

PROVIDER: S-EPMC6422928 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature