Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing

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

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.

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Paper Citation


in Harvard Style

Champion M., Hlady R., Yan H., Evans J., Nie J., Lee J., Bogenberger J., Nandakumar K., Davila J., Moore R., Nair A., O'Brien D., Zhu Y., Kortüm K., Ordog T., Zhang Z., Joseph R., Stewart A., Kocher J., Jonasch E., Robertson K., Tibes R. and H. Ho T. (2015). Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 163-170. DOI: 10.5220/0005248001630170


in Bibtex Style

@conference{bioinformatics15,
author={Mia D. Champion and Ryan A. Hlady and Huihuang Yan and Jared Evans and Jeff Nie and Jeong-Heon Lee and James M. Bogenberger and Kannabiran Nandakumar and Jaime Davila and Raymond Moore and Asha Nair and Daniel O'Brien and Yuan-Xiao Zhu and K. Martin Kortüm and Tamas Ordog and Zhiguo Zhang and Richard W. Joseph and A. Keith Stewart and Jean-Pierre Kocher and Eric Jonasch and Keith D. Robertson and Raoul Tibes and Thai H. Ho},
title={Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={163-170},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005248001630170},
isbn={978-989-758-070-3},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing
SN - 978-989-758-070-3
AU - Champion M.
AU - Hlady R.
AU - Yan H.
AU - Evans J.
AU - Nie J.
AU - Lee J.
AU - Bogenberger J.
AU - Nandakumar K.
AU - Davila J.
AU - Moore R.
AU - Nair A.
AU - O'Brien D.
AU - Zhu Y.
AU - Kortüm K.
AU - Ordog T.
AU - Zhang Z.
AU - Joseph R.
AU - Stewart A.
AU - Kocher J.
AU - Jonasch E.
AU - Robertson K.
AU - Tibes R.
AU - H. Ho T.
PY - 2015
SP - 163
EP - 170
DO - 10.5220/0005248001630170