Thesis Defense: Identifying chromatin interactions at high spatial resolution
Christopher Reeder, MIT CSAIL
Date: Friday, April 11, 2014
Time: 1:00 PM to 3:00 PM Note: all times are in the Eastern Time Zone
Host: David Gifford, Tommi Jaakkola, and Ernest Fraenkel
Contact: Patrice Macaluso, firstname.lastname@example.org
Speaker URL: None
TALK: Identifying chromatin interactions at high spatial resolution
We present two complementary computational methods for identifying chromatin interactions at high spatial resolution from ChIA-PET data. We introduce Sprout which is a hierarchical probabilistic model that discovers high confidence interactions between accurately located binding events. We apply Sprout to CTCF ChIA-PET data from mouse embryonic stem cells and demonstrate that Sprout discovers interactions that are more consistently supported by biological replicates than the competing method. Based on the observation that two general classes of ChIA-PET data exist for which different modeling assumptions are appropriate, we also introduce Germ which models genome-wide distributions of protein joint occupancy. We demonstrate that the locations that Germ identifies as interacting with the transcription start sites of genes accurately align with ChIP-Seq data that are associated with active enhancers. Finally, we apply Germ to RNA Polymerase II ChIA-PET data from mouse embryonic stem cells and motor neuron progenitors in order to characterize the differential usage of enhancers during motor neuron development.
Created by Patrice Macaluso at Thursday, April 10, 2014 at 3:26 PM.