Gruber, Andreas J. and Schmidt, Ralf and Ghosh, Souvik and Martin, Georges and Gruber, Andreas R. and van Nimwegen, Erik and Zavolan, Mihaela. (2018) Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome biology, 19 (1). p. 44.
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Official URL: https://edoc.unibas.ch/63459/
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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.
| Faculties and Departments: | 05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan) 05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen) |
|---|---|
| UniBasel Contributors: | Zavolan, Mihaela and Gruber, Andreas J. and Ghosh, Souvik and Schmidt, Ralf and Martin, Georges and van Nimwegen, Erik |
| Item Type: | Article, refereed |
| Article Subtype: | Research Article |
| ISSN: | 1474-760X |
| Note: | Publication type according to Uni Basel Research Database: Journal article |
| Identification Number: |
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| Last Modified: | 27 Apr 2020 18:02 |
| Deposited On: | 27 Apr 2020 18:02 |
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