Thesis Defense: Identifying chromatin interactions at high spatial resolution

Speaker: 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

Public: Yes

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Host: David Gifford, Tommi Jaakkola, and Ernest Fraenkel

Contact: Patrice Macaluso, macaluso@csail.mit.edu

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Reminders to: seminars@csail.mit.edu, bioinfo-seminar@lists.csail.mit.edu

Reminder Subject: 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.

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Created by Patrice Macaluso at Thursday, April 10, 2014 at 3:26 PM.