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.
List of abbreviations
- BCLA
- Bladder Urothelial Carcinoma
- BRCA
- Breast Invasive Carcinoma
- COAD
- Colon Adenocarcinoma
- ESCA
- Esophageal Carcinoma
- GBM
- Glioblastoma Multiforme
- HNSC
- Head and Neck Squamous Cell Carcinoma
- KICH
- Kidney Chromophobe
- KIRC
- Kidney Renal Clear Cell Carcinoma
- KIRP
- Kidney Renal Papillary Cell Carcinoma
- LIHC
- Liver Hepatocellular Carcinoma
- LUAD
- Lung Adenocarcinoma
- LUSC
- Lung Squamous Cell Carcinoma
- PRAD
- Prostate Adenocarcinoma
- READ
- Rectum Adenocarcinoma
- STAD
- Stomach Adenocarcinoma
- THCA
- Thyroid Carcinoma
- UCEC
- Uterine Corpus Endometrial Carcinoma
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Posted December 01, 2017.
Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC
