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Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO cells as a global re‐expression model

Author
Organization
Abstract
Short Abstract: Background: IT has been shown before that gene promoter methylation suppress expression of the downstream gene. This mechanism is involved in a series of diseases such as for example cancer, where tumor suppressor genes can be methylated and thus suppressed. Methodology: We did a genome-wide methylation analysis of a colon cancer cell line (HCT116) using Methyl-Binding-Domain (MDB) capturing followed by next-generation sequencing. We also did a genome-wide totalRNA (mRNA, miRNA, snoRNA ...) analysis of a colon cancer cell line (HCT116) and of a HCT116 cell line with both DNMT1 and DNMT3B knocked out (DKO) using directional next-generation RNA sequencing. Both the methylation and RNA were analysed using Illumina next-generation sequencing technology. Results: Using computational analysis and comparing the expression in HCT116 and DKO, and taking the methylation profile into account, we were able to identify pathways that are directly regulated by the methylation and pathways that are regulated in an indirect fashion. Furthermore, we were able to confirm known methylation regulated protein coding genes, miRNAs (e.g. hsa-mir-146a) and snoRNAs (e.g. SNORD116) in a single comprehensive sequencing experiment. We also could identify exons and alternative transcripts of which the expression is regulated by methylation, confirming the link between alternative splicing and methylation.
Keywords
MBD-sequencing, Cancer, RNA-sequencing, Bioinformatics, Re-expression, Next-generation sequencing

Citation

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Chicago
De Schrijver, Joachim, Geert Trooskens, Linda JW Bosch, Pierre Dehan, Beatriz Carvalho, Leander Van Neste, Gerrit Meijer, Steve Baylin, and Wim Van Criekinge. 2012. “Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO Cells as a Global Re‐expression Model.” In Intelligent Systems for Molecular Biology, 20th Annual International Conference, Abstracts.
APA
De Schrijver, Joachim, Trooskens, G., Bosch, L. J., Dehan, P., Carvalho, B., Van Neste, L., Meijer, G., et al. (2012). Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO cells as a global re‐expression model. Intelligent Systems for Molecular Biology, 20th Annual international conference, Abstracts. Presented at the 20th Annual international conference on Intelligent Systems for Molecular Biology (ISMB 2012).
Vancouver
1.
De Schrijver J, Trooskens G, Bosch LJ, Dehan P, Carvalho B, Van Neste L, et al. Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO cells as a global re‐expression model. Intelligent Systems for Molecular Biology, 20th Annual international conference, Abstracts. 2012.
MLA
De Schrijver, Joachim, Geert Trooskens, Linda JW Bosch, et al. “Genome‐wide RNA‐ and MBD‐sequencing in HCT116 and DKO Cells as a Global Re‐expression Model.” Intelligent Systems for Molecular Biology, 20th Annual International Conference, Abstracts. 2012. Print.
@inproceedings{3070530,
  abstract     = {Short Abstract: Background: IT has been shown before that gene promoter methylation suppress expression of the downstream gene. This mechanism is involved in a series of diseases such as for example cancer, where tumor suppressor genes can be methylated and thus suppressed. 
Methodology: We did a genome-wide methylation analysis of a colon cancer cell line (HCT116) using Methyl-Binding-Domain (MDB) capturing followed by next-generation sequencing. We also did a genome-wide totalRNA (mRNA, miRNA, snoRNA ...) analysis of a colon cancer cell line (HCT116) and of a HCT116 cell line with both DNMT1 and DNMT3B knocked out (DKO) using directional next-generation RNA sequencing. Both the methylation and RNA were analysed using Illumina next-generation sequencing technology. 
Results: Using computational analysis and comparing the expression in HCT116 and DKO, and taking the methylation profile into account, we were able to identify pathways that are directly regulated by the methylation and pathways that are regulated in an indirect fashion. Furthermore, we were able to confirm known methylation regulated protein coding genes, miRNAs (e.g. hsa-mir-146a) and snoRNAs (e.g. SNORD116) in a single comprehensive sequencing experiment. We also could identify exons and alternative transcripts of which the expression is regulated by methylation, confirming the link between alternative splicing and methylation.},
  articleno    = {poster J02},
  author       = {De Schrijver, Joachim and Trooskens, Geert and Bosch, Linda JW and Dehan, Pierre and Carvalho, Beatriz and Van Neste, Leander and Meijer, Gerrit and Baylin, Steve and Van Criekinge, Wim},
  booktitle    = {Intelligent Systems for Molecular Biology, 20th Annual international conference, Abstracts},
  language     = {eng},
  location     = {Long Beach, CA, USA},
  title        = {Genome\unmatched{2010}wide RNA\unmatched{2010} and MBD\unmatched{2010}sequencing in HCT116 and DKO cells as a global re\unmatched{2010}expression model},
  url          = {https://www.iscb.org/cms\_addon/conferences/ismb2012/posterlist.php?cat=J},
  year         = {2012},
}