Suppression subtractive hybridization cDNA libraries to identify differentially expressed genes from contrasting fish habitats

• Published in: Marine biotechnology (New York, N.Y.) N.Y.), 2004-08, Vol.6 (4), p.386-399
• Main Authors: Straub, Peter F, Higham, Mary L, Tanguy, Arnaud, Landau, Brenda J, Phoel, William C, Hales, Jr, L Stanton, Thwing, Theodore K M
• Format: Article
• Language: English
• Subjects: Animals; Anthropogenic factors; Base Sequence; Brackish; DNA Primers; Environment; Estuaries; Flounder - genetics; Flounder - metabolism; Gene expression; Gene Expression Regulation; Gene Library; Genetic Markers - genetics; Habitats; Hybridization; Immune response; Libraries; Liver - metabolism; Molecular Sequence Data; New Jersey; Nucleic Acid Hybridization - methods; Pleuronectiformes; Polymerase Chain Reaction - methods; Proteins; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, DNA; Water Pollution, Chemical; Xenobiotics
• ISSN: 1436-2228; 1436-2236
• DOI: 10.1007/s10126-004-3146-6

Suppression subtractive hybridization complementary DNA libraries identified differentially expressed genes in liver tissue of winter flounder collected from the highly impacted Raritan-Hudson estuary versus those from less industrialized estuaries farther south in New Jersey. Distinct transcript profiles emerged in the fish from these different habitats. A total of 251 clones from the forward (upregulated with anthropogenic impact) and reverse (downregulated with anthropogenic impact) subtracted libraries were sequenced. In the upregulated library immune response transcripts, including complement C-3, C-7, factor H, factor Bf/C2, differentially regulated trout protein 1, and the antimicrobial hepcidin, indicated the pollution-impacted fish were under a high viral or bacterial load. Transcripts for cytochrome P450 1A, P450 3A, and glutathione S-transferase, important components of phase I and II metabolism of xenobiotics, were found in the upregulated-with-pollution library. Vitellogenins I and II and egg envelope protein (zp) appeared to be downregulated. A homologue of the tumor suppressor p33(ING1) (down) and hepatocyte growth factor-like protein (up) may indicate liver damage or hepatocellular carcinoma or hepatoma. These expression patterns, confirmed by quantitative polymerase chain reaction, indicate that transcript analysis is a useful method for assessing the health of local habitats and the organisms therein.