Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing

Mia D. Champion, Ryan A. Hlady, Huihuang D Yan, Jared Evans, Jeff Nie, Jeong Heon Lee, James Bogenberger, Kannabiran Nandakumar, Jaime Davila, Raymond Moore, Asha Nair, Daniel O'Brien, Yuan Xiao Zhu, K. Martin Kortum, Tamas Ordog, Zhiguo Zhang, Richard W Joseph, Alexander Keith Stewart, Jean-Pierre Kocher, Eric JonaschKeith D Robertson, Raoul Tibes, Thai H Ho

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Epigenetic modifications are associated with the regulation of co/post-transcriptional processing and differential transcript isoforms are known to be important during cancer progression. It remains unclear how disruptions of chromatin-based modifications contribute to tumorigenesis and how this knowledge can be leveraged to develop more potent treatment strategies that target specific isoforms or other products of the co/post-transcriptional regulation pathway. Rapid developments in all areas of next-generation sequencing (DNA, RNA-seq, ChIP-seq, Methyl-CpG, etc.) have provided new opportunities to develop novel integration and data-mining approaches, and also allows for exciting hypothesis driven bioinformatics and computational studies. Here, we present a program that we developed and summarize the results of applying our methods to analyze datasets from patient matched tumor or normal (T/N) paired samples, as well as cell lines that were either sensitive or resistant (S/R) to treatment with an anti-cancer drug, 5-Azacytidine (http://sourceforge.net/projects/chiprnaseqpro/). We discuss additional options for user-defined approaches and general guidelines for simultaneously analyzing and annotating epigenetic and RNA-seq datasets in order to identify and rank significant regions of epigenetic deregulation associated with aberrant splicing and RNA-editing.

Original languageEnglish (US)
Title of host publicationBIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015
PublisherSciTePress
Pages163-170
Number of pages8
ISBN (Print)9789897580703
StatePublished - 2015
Event6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015 - Lisbon, Portugal
Duration: Jan 12 2015Jan 15 2015

Other

Other6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015
CountryPortugal
CityLisbon
Period1/12/151/15/15

Keywords

  • Alu elements
  • Bioinformatics
  • ChIP-seq
  • Co/post-transcriptional processing
  • DNAme
  • Epigenetic modification
  • Methyl-CpG
  • Methylation
  • NMD
  • RNA-editing
  • RNA-seq
  • Splicing
  • Transcriptome

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Architecture

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