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

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2018
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Schmidt, Ralf
Ghosh, Souvik
Martin, Georges
Gruber, Andreas R.
van Nimwegen, Erik
Zavolan, Mihaela
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Genome biology. BioMed Central. 2018, 19(1), 44. ISSN 1465-6906. eISSN 1465-6914. Available under: doi: 10.1186/s13059-018-1415-3
Zusammenfassung

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.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Cleavage and polyadenylation, APA, CFIm, KAPAC, PAQR, HNRNPC, PTBP1, Prostate adenocarcinoma, Glioblastoma, Colon adenocarcinoma
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Zitieren
ISO 690GRUBER, 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. 2018, 19(1), 44. ISSN 1465-6906. eISSN 1465-6914. Available under: doi: 10.1186/s13059-018-1415-3
BibTex
@article{Gruber2018Disco-51014,
  year={2018},
  doi={10.1186/s13059-018-1415-3},
  title={Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC},
  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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