Research Projects

Genome-Wide Analysis of Alternative Polyadenylation Sites in Various Human Cell Types

Speaker:Dina Hafez
dhafez at cs.duke.edu
Date: Friday, April 27, 2012
Time: 1:30pm - 3:00pm
Location: North 311, Duke

Abstract

The 5’ and 3’ untranslated regions (UTRs) in eukaryotic messenger RNA (mRNA) incorporate major regulatory elements that act as platforms for the assembly of protein complexes to the mRNA, thus generating ribonucleoparticles (mRNPs). The 3’UTR is typically known for its role in regulating multiple aspects of mRNA metabolism and stability. An mRNA can be processed into a number of different isoforms by steps such as alternative splicing and polyadenylation. Alternative splicing has long been known as a mechanism for generating functional diversity in the cellular proteome; alternative polyadenylation (APA) has an impact on mRNA post transcriptional regulation, due to various cis-acting elements located in the 3’UTR region. More recently, it has been recognized that APA plays important regulatory roles in physiological and pathological processes. In this project, we identified poly(A) sites using a newly developed RNA-seq protocol for capturing poly(A) sites. We applied linear model to determine specific poly(A) sites and built a kernalized SVM classifier to predict constitutive poly(A) sites, as well as alternative sites in different human cell types using string kernels.
Advisor(s): Uwe Ohler
Alexander Hartemink, Raluca Gordan