Accurate prediction of boundaries of high resolution topologically associated domains (TADs) in fruit flies using deep learning.

ABSTRACT: Genomes are organized into self-interacting chromatin regions called topologically associated domains (TADs). A significant number of TAD boundaries are shared across multiple cell types and conserved across species. Disruption of TAD boundaries may affect the expression of nearby genes and could lead to several diseases. Even though detection of TAD boundaries is important and useful, there are experimental challenges in obtaining high resolution TAD locations. Here, we present computational prediction of TAD boundaries from high resolution Hi-C data in fruit flies. By extensive exploration and testing of several deep learning model architectures with hyperparameter optimization, we show that a unique deep learning model consisting of three convolution layers followed by a long short-term

SUBMITTER: Henderson J 

PROVIDER: S-EPMC6648328 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature