Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq
- Guorong Xu1,
- Claire Fewell2,
- Christopher Taylor1,3,
- Nan Deng1,
- Dale Hedges4,
- Xia Wang2,
- Kun Zhang5,
- Michelle Lacey6,
- Haitao Zhang2,
- Qinyan Yin2,
- Jennifer Cameron2,
- Zhen Lin2,
- Dongxiao Zhu1,3 and
- Erik K. Flemington2
- 1Department of Computer Science, University of New Orleans, New Orleans, Louisiana 70148, USA
- 2Department of Pathology, Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, Louisiana 70112, USA
- 3Research Institute for Children, Children's Hospital, New Orleans, New Orleans, Louisiana 70118, USA
- 4Miami Institute of Human Genomics, Miami, Florida 33136, USA
- 5Department of Computer Science, Xavier University of New Orleans, New Orleans, Louisiana 70125, USA
- 6Department of Mathematics, Tulane University and Tulane Cancer Center, New Orleans, Louisiana 70112, USA
Abstract
Previous studies have demonstrated the utility of microarray expression analysis to identify potential microRNA targets. Nevertheless, technical limitations intrinsic to this platform constrain its ability to fully exploit the potential of assessing transcript level changes to explore microRNA targetomes. High-throughput multiplexed Illumina-based next-generation sequencing (NGS) provides a digital readout of absolute transcript levels and imparts a higher level of accuracy and dynamic range than microarray platforms. We used Illumina NGS to analyze transcriptome changes induced by the human microRNA MIR155. This analysis resulted in a larger inferred targetome than similar studies carried out using microarray platforms. A comparison with 3′ UTR reporter data demonstrated general concordance between NGS and corresponding 3′ UTR reporter results. Nonharmonious results were investigated more deeply using transcript structure information assembled from the NGS data. This analysis revealed that transcript structure plays a substantial role in mitigated targeting and in frank targeting failures. With its high level of accuracy, its broad dynamic range, its utility in assessing transcript structure, and its capacity to accurately interrogate global direct and indirect transcriptome changes, NGS is a useful tool for investigating the biology and mechanisms of action of microRNAs.
Keywords
Footnotes
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Reprint requests to: Erik K. Flemington, Department of Pathology, Tulane University Health Sciences Center and Tulane Cancer Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA; e-mail: eflemin{at}tulane.edu; fax: (504) 988-1167; or Dongxiao Zhu, Department of Computer Science, University of New Orleans, Lakefront, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; e-mail: dzhu{at}cs.uno.edu; fax: (504) 280-2406.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2194910.
- Received March 25, 2010.
- Accepted May 14, 2010.
- Copyright © 2010 RNA Society
Freely available online through the RNA Open Access option.