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 Jonasch & 3 others Keith 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

Fingerprint

RNA Editing
Deregulation
Bioinformatics
Computational Biology
RNA
Epigenomics
Protein Isoforms
RNA Sequence Analysis
Azacitidine
Neoplasms
Data Mining
DNA Sequence Analysis
Chromatin
Data mining
Tumors
Carcinogenesis
DNA
Cells
Guidelines
Cell Line

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

Cite this

Champion, M. D., Hlady, R. A., Yan, H. D., Evans, J., Nie, J., Lee, J. H., ... Ho, T. H. (2015). Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. In BIOINFORMATICS 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 (pp. 163-170). SciTePress.

Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. / Champion, Mia D.; Hlady, Ryan A.; Yan, Huihuang D; Evans, Jared; Nie, Jeff; Lee, Jeong Heon; Bogenberger, James; Nandakumar, Kannabiran; Davila, Jaime; Moore, Raymond; Nair, Asha; O'Brien, Daniel; Zhu, Yuan Xiao; Kortum, K. Martin; Ordog, Tamas; Zhang, Zhiguo; Joseph, Richard W; Stewart, Alexander Keith; Kocher, Jean-Pierre; Jonasch, Eric; Robertson, Keith D; Tibes, Raoul; Ho, Thai H.

BIOINFORMATICS 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. SciTePress, 2015. p. 163-170.

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

Champion, MD, Hlady, RA, Yan, HD, Evans, J, Nie, J, Lee, JH, Bogenberger, J, Nandakumar, K, Davila, J, Moore, R, Nair, A, O'Brien, D, Zhu, YX, Kortum, KM, Ordog, T, Zhang, Z, Joseph, RW, Stewart, AK, Kocher, J-P, Jonasch, E, Robertson, KD, Tibes, R & Ho, TH 2015, Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. in BIOINFORMATICS 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. SciTePress, pp. 163-170, 6th International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2015, Lisbon, Portugal, 1/12/15.
Champion MD, Hlady RA, Yan HD, Evans J, Nie J, Lee JH et al. Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. In BIOINFORMATICS 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. SciTePress. 2015. p. 163-170
Champion, Mia D. ; Hlady, Ryan A. ; Yan, Huihuang D ; Evans, Jared ; Nie, Jeff ; Lee, Jeong Heon ; Bogenberger, James ; Nandakumar, Kannabiran ; Davila, Jaime ; Moore, Raymond ; Nair, Asha ; O'Brien, Daniel ; Zhu, Yuan Xiao ; Kortum, K. Martin ; Ordog, Tamas ; Zhang, Zhiguo ; Joseph, Richard W ; Stewart, Alexander Keith ; Kocher, Jean-Pierre ; Jonasch, Eric ; Robertson, Keith D ; Tibes, Raoul ; Ho, Thai H. / Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. BIOINFORMATICS 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. SciTePress, 2015. pp. 163-170
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AU - Champion, Mia D.

AU - Hlady, Ryan A.

AU - Yan, Huihuang D

AU - Evans, Jared

AU - Nie, Jeff

AU - Lee, Jeong Heon

AU - Bogenberger, James

AU - Nandakumar, Kannabiran

AU - Davila, Jaime

AU - Moore, Raymond

AU - Nair, Asha

AU - O'Brien, Daniel

AU - Zhu, Yuan Xiao

AU - Kortum, K. Martin

AU - Ordog, Tamas

AU - Zhang, Zhiguo

AU - Joseph, Richard W

AU - Stewart, Alexander Keith

AU - Kocher, Jean-Pierre

AU - Jonasch, Eric

AU - Robertson, Keith D

AU - Tibes, Raoul

AU - Ho, Thai H

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

KW - Alu elements

KW - Bioinformatics

KW - ChIP-seq

KW - Co/post-transcriptional processing

KW - DNAme

KW - Epigenetic modification

KW - Methyl-CpG

KW - Methylation

KW - NMD

KW - RNA-editing

KW - RNA-seq

KW - Splicing

KW - Transcriptome

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M3 - Conference contribution

SN - 9789897580703

SP - 163

EP - 170

BT - BIOINFORMATICS 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

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