The Authors: Rebecca Cullum studies gene expression and regulation during mouse development as a Research Technician at the BC Cancer Agency. Olivia Alder, PhD, is currently a Postdoctoral Fellow at BC Cancer Agency with a background in epigenetics and transcriptional regulation. Pamela Hoodless, PhD, is a Senior Scientist at the BC Cancer Agency and Associate Professor in the Department of Medical Genetics at the University of British Columbia with an interest in applying genomic technology to embryology. Dr Hoodless is a Senior Scholar with the Michael Smith Foundation for Health Research.
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The next generation: Using new sequencing technologies to analyse gene regulation
Article first published online: 27 JAN 2011
DOI: 10.1111/j.1440-1843.2010.01899.x
© 2011 The Authors. Respirology © 2011 Asian Pacific Society of Respirology
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How to Cite
CULLUM, R., ALDER, O. and HOODLESS, P. A. (2011), The next generation: Using new sequencing technologies to analyse gene regulation. Respirology, 16: 210–222. doi: 10.1111/j.1440-1843.2010.01899.x
SERIES EDITOR: DARRYL KNIGHT
Publication History
- Issue published online: 27 JAN 2011
- Article first published online: 27 JAN 2011
- Accepted manuscript online: 16 NOV 2010 04:58AM EST
- Received 10 August 2010; invited to revise 27 September 2010; revised 12 October 2010; accepted 4 November 2010.
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Keywords:
- chromatin immunoprecipitation;
- gene expression profiling;
- gene expression regulation;
- genomics;
- sequence analysis
ABSTRACT
Next generation sequencing (NGS) has pushed back the limitations of prior sequencing technologies to advance genomic knowledge infinitely by allowing cost-effective, rapid sequencing to become a reality. Genome-wide transcriptional profiling can be achieved using NGS with either Tag-Seq, in which short tags of cDNA represent a gene, or RNA-Seq, in which the entire transcriptome is sequenced. Furthermore, the level and diversity of miRNA within different tissues or cell types can be monitored by specifically sequencing small RNA. The biological mechanisms underlying differential gene regulation can also be explored by coupling chromatin immunoprecipitation with NGS (ChIP-Seq). Using this methodology genome-wide binding sites for transcription factors, RNAP II, epigenetic modifiers and the distribution of modified histones can be assessed. The superior, high-resolution data generated by adopting this sequencing technology allows researchers to distinguish the precise genomic location bound by a protein and correlate this with observed gene expression patterns. Additional methods have also been established to examine other factors influencing gene regulation such as DNA methylation or chromatin conformation on a genome-wide scale. Within any research setting, these techniques can provide relevant data and answer numerous questions about gene expression and regulation. The advances made by pairing NGS with strategic experimental protocols will continue to impact the research community.