Genome biologySystems BiologyPeer-reviewed journal article
Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC
Andreas J GruberiD, Ralf Schmidt, Souvik GhoshiD, Georges Martin, Erik van NimwegeniD, Mihaela ZavolaniD
Abstract
3 UTR length is regulated in relation to cellular state. To uncover key regulators of poly(A) site (PAS) use in specific conditions, we have developed PAQR, a method for quantifying PAS use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on PAS choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovered sequence 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 PAS choice in glioblastoma.
- organism: human
- assay: bulk RNA-seq
- research focus: differential expression
- research focus: gene regulatory network inference
- approach: statistical model
- Citations
- 74
- FWCI
- 3.02
- Field percentile
- top 7%
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation
Zhuyi Xue, René L. Warren, … İnanç Birol·BMC GenomicsPeer-reviewed·Jul 13, 2018
- APA-Scan: Detection and Visualization of 3'-UTR APA with RNA-seq and 3'-end-seq Data
Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, … Wei Zhang·BMC BioinformaticsPeer-reviewed·Sep 28, 2022
- A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation
Andreas J Gruber, Ralf Schmidt, … Mihaela Zavolan·bioRxiv·Nov 26, 2015
- Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism
Dominik Bürri, Mihaela Zavolan·RNAPeer-reviewed·Sep 14, 2021
- LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival
Raeann Goering, Krysta L. Engel, … J. Matthew Taliaferro·BMC GenomicsPeer-reviewed·Jun 26, 2021
- Activation and inhibition of nonsense-mediated mRNA decay controls the abundance of alternative polyadenylation products
Aparna Kishor, Sarah E Fritz, … J. Robert Hogg·Nucleic Acids ResearchPeer-reviewed·May 30, 2020