Target Prediction Algorithms and Bioinformatics Resources for miRNA Studies - MicroRNAs as Tools in Biopharmaceutical Production - page 29

Chapter 3
Target Prediction Algorithms and Bioinformatics
Resources for miRNA Studies

Colin Clarke, Niall Barron, Mark Gallagher, Michael Henry, Paula Meleady
and Martin Clynes

Abstract The recent publication of the Chinese hamster ovary (CHO) genome has
heralded the beginning of an exciting new era of research in this industrially impor-
tant cell line. Advances in our understanding of CHO at the molecular level have
the potential to facilitate the development of modified cell lines and biomarkers to
increase the efficiency of recombinant protein production processes. In recent years
there has been growing interest in the function of small non-coding RNA molecules,
known as microRNAs (miRNAs), as targets to enable multigene CHO cell engineer-
ing. To date, miRNAs have been shown to be dysregulated in a number of processes
including cell growth and apoptosis.
Bioinformatics has proven to be an essential supporting technology for miRNA
based studies. In this chapter, we review a new class of miRNA specific in-silico
tool developed to predict which mRNAs a particular miRNA targets in order to de-
termine the impact of a miRNA on biological function. A range of popular miRNA
target prediction algorithms are presented, their underlying principles described and
performance assessed. In addition, publically available repositories of miRNA se-
quence, expression profiling and target data are highlighted. Finally, examples of the
utilisation of these tools to study CHO cells are presented.

Keywords MicroRNA · Bioinformatics · Target prediction algorithm · MicroRNA

data repository · CHO · Bioprocess

3.1 Introduction

The study of miRNA-mediated regulation of CHO cells in industrial culture has
progressed rapidly despite the fact that until recently no genome sequence was avail-
able (Xu et al. 2011 ). In contrast to other “omics” platforms, the high degree of
conservation of miRNAs across mammalian species has allowed the utilisation of

C. Clarke ( ) M. Clynes

National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
e-mail: [e-mail]

· N. Barron · M. Gallagher · M. Henry · P. Meleady ·