Journal Article

Coping with Cold: An Integrative, Multitissue Analysis of the Transcriptome of a Poikilothermic Vertebrate

Cossins, Andrew R., Rogers, Jane, Fraser, E. Jane, Fang, Yongxiang, Li, Weizhong, Brass, Andrew, Taylor, Ruth R., Gracey, Andrew Y., Brown, Patrick O.

2004

Overview

How do organisms respond adaptively to environmental stress? Although some gene-specific responses have been explored, others remain to be identified, and there is a very poor understanding of the system-wide integration of response, particularly in complex, multitissue animals. Here, we adopt a transcript screening approach to explore the mechanisms underpinning a major, whole-body phenotypic transition in a vertebrate animal that naturally experiences extreme environmental stress. Carp were exposed to increasing levels of cold, and responses across seven tissues were assessed by using a microarray composed of 13,440 cDNA probes. A large set of unique cDNAs (≈3,400) were affected by cold. These cDNAs included an expression signature common to all tissues of 252 up-regulated genes involved in RNA processing, translation initiation, mitochondrial metabolism, proteasomal function, and modification of higher-order structures of lipid membranes and chromosomes. Also identified were large numbers of transcripts with highly tissue-specific patterns of regulation. By unbiased profiling of gene ontologies, we have identified the distinctive functional features of each tissue's response and integrate them into a comprehensive view of the whole-body transition from one strongly adaptive phenotype to another. This approach revealed an expression signature suggestive of atrophy in cooled skeletal muscle. This environmental genomics approach by using a well studied but nongenomic species has identified a range of candidate genes endowing thermotolerance and reveals a previously unrecognized scale and complexity of responses that impacts at the level of cellular and tissue function.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Adaptation, Physiological - genetics / Animals / Biological Sciences / Carp / Carps - genetics / Carps - physiology / Chromosomes / Cold / Cold Temperature / Complementary DNA / Cooling / Deoxyribonucleic acid / DNA / DNA Probes / DNA, Complementary / Environmental stress / Fish / Freshwater / Gene Expression Profiling / Gene expression regulation / Genes / Genetics / Liver / Molecular Sequence Data / Oligonucleotide Array Sequence Analysis / Principal components analysis / RNA / RNA, Messenger - genetics / Skeletal muscle / Stress / Tissues / Vertebrates / Yeasts