Departmental Papers (Department of Systems Pharmacology and Translational Therapeutics)
Document Type
Journal Article
Date of this Version
2017
Publication Source
PLOS Computational Biology
Volume
13
Issue
6
DOI
10.1371/journal.pcbi.1005602
Abstract
A compelling body of literature, based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction. It is now critical to develop highly innovative computational strategies to reveal the relevant regulatory transcriptional mechanisms that may underlie neuropsychiatric disease. We have analyzed chromatin regulation of alternative splicing, which is implicated in cocain exposure in mice. Recent literature has described chromatin-regulated alternative splicing, suggesting a novel function for drug-induced neuroepigenetic remodeling. However, the extent of the genome-wide association between particular histone modifications and alternative splicing remains unexplored. To address this, we have developed novel computational approaches to model the association between alternative splicing and histone posttranslational modifications in the nucleus accumbens (NAc), a brain reward region. Using classical statistical methods and machine learning to combine ChIP-Seq and RNA-Seq data, we gound that specific histone modifications are strongly associated with various aspects of differential splicing. H3K36me3 and H3K4me1 have the strongest association with splicing indicating they play a significant role in alternative splicing in brain reward tissue.
Copyright/Permission Statement
© 2017 Hu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Recommended Citation
Hu, Qiwen; Kim, Eun J.; Feng, Jian; Grant, Gregory R.; and Heller, Elizabeth A., "Histone Posttranslational Modifications Predict Specific Alternative Exon Subtypes in Mammalian Brain" (2017). Departmental Papers (Department of Systems Pharmacology and Translational Therapeutics). 7.
https://repository.upenn.edu/pharmacology_papers/7
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Computational Biology Commons, Neuroscience and Neurobiology Commons, Pharmacology, Toxicology and Environmental Health Commons, Pharmacy and Pharmaceutical Sciences Commons, Translational Medical Research Commons
Date Posted: 24 January 2018
This document has been peer reviewed.