Genomics and Environmental Hypoxia: What (and How) We Can Learn from the Transcriptome

Abstract

Abstract

Rupert, Jim L. Genomics and environmental hypoxia: what (and how) we can learn from the transcriptome. High Alt. Med. & Biol. 9:115–122, 2008.—Recent developments in molecular biology have shown that the classic “one gene, one RNA, one protein” model is inadequate to account for the transcriptional complexity apparent in higher organisms. Current understanding of the transcriptome (the -ome term for the entire complement of transcripts in a cell, tissue, or organism) suggests that genes can produce many different transcripts due to variable start and termination sites and alternate splicing, and that much of the extragenic (the region believed to lay outside genes) genome is also transcribed, producing a bewildering array of noncoding RNAs (ncRNA), including antisense transcripts and microRNAs that are thought to be involved in the posttranscriptional regulation of gene expression. As part of the attempt to understand this plethora of biological information, researchers have developed new technologies that permit the assessment of thousands of transcripts simultaneously. The resulting transcription profile provides a high-resolution and highly informative snapshot of gene activity in the tissue. The two most common of these methodological strategies are microarrays, which are based on hybridization technology, and serial (or cap) analysis of gene expression (SAGE or CAGE), which is based on DNA sequencing. This paper reviews the basic principles underlying these technologies and describes how they have been applied to understanding the molecular events that underlie the response to environmental hypoxia.