Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC
| Type of Publication: | Journal article |
| Publication status: | Published |
| URI (citable link): | http://nbn-resolving.de/urn:nbn:de:bsz:352-2-4vizwhlwnd941 |
| Author: | Gruber, Andreas J.; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R.; van Nimwegen, Erik; Zavolan, Mihaela |
| Year of publication: | 2018 |
| Published in: | Genome biology ; 19 (2018), 1. - 44. - BioMed Central. - ISSN 1465-6906. - eISSN 1465-6914 |
| Pubmed ID: | 29592812 |
| DOI (citable link): | https://dx.doi.org/10.1186/s13059-018-1415-3 |
| Summary: |
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.
|
| Subject (DDC): | 570 Biosciences, Biology |
| Keywords: | Cleavage and polyadenylation, APA, CFIm, KAPAC, PAQR, HNRNPC, PTBP1, Prostate adenocarcinoma, Glioblastoma, Colon adenocarcinoma |
| Link to License: | Attribution 4.0 International |
| Refereed: | Yes |
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GRUBER, Andreas J., Ralf SCHMIDT, Souvik GHOSH, Georges MARTIN, Andreas R. GRUBER, Erik VAN NIMWEGEN, Mihaela ZAVOLAN, 2018. Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. In: Genome biology. BioMed Central. 19(1), 44. ISSN 1465-6906. eISSN 1465-6914. Available under: doi: 10.1186/s13059-018-1415-3
@article{Gruber2018Disco-51014, title={Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC}, year={2018}, doi={10.1186/s13059-018-1415-3}, number={1}, volume={19}, issn={1465-6906}, journal={Genome biology}, author={Gruber, Andreas J. and Schmidt, Ralf and Ghosh, Souvik and Martin, Georges and Gruber, Andreas R. and van Nimwegen, Erik and Zavolan, Mihaela}, note={Article Number: 44} }
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