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Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC.

Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC.
Author Information (click to view)

Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M,


Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M, (click to view)

Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M,

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Genome biology 2018 03 2819(1) 44 doi 10.1186/s13059-018-1415-3

Abstract

3′ Untranslated regions (3′ UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma.

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