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Suppression Subtractive Hybridization cDNA Libraries to Identify Differentially Expressed Genes from Contrasting Fish Habitats

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Abstract

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 p33ING1 (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.

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Acknowledgments

We acknowledge Steve Evert and Stockton’s Nacote Creek Field Station, Bruce and Barbara Boyd of The Marine Academy of Science & Technology, and the RV Blue Sea for assistance in collection of fish. Also, the assistance of Dr. David W. Towle of the Marine DNA Sequencing and Analysis Facility of the Mt. Desert Island Biological Laboratory (MDIBL) was invaluable. This research was supported by The Richard Stockton College of New Jersey under a Distinguished Faculty Fellowship, The National Science Foundation under grants DBI-MRI-0116165 and DBI-REU-0097635, Mt. Desert Island Biological Laboratory, under a New Investigator Award supported by the National Institutes of Environmental Health Science grant NIEHS P30 ESO3828-18 to the Center for Membrane Toxicity Studies, and the National Sea Grant College Program of the U.S. Department of Commerce’s National Oceanic and Atmospheric Administration under NOAA grant NA 16RG1047. The views expressed herein do not necessarily reflect the views of any of those organizations. This is a publication of New Jersey Sea Grant, NJSG-03-525.

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Authors and Affiliations

  1. Natural Sciences & Math, Richard Stockton College, Pomona, New Jersey, 08240, USA

    Peter F. Straub, Mary L. Higham, William C. Phoel & L. Stanton Hales Jr.

  2. Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, 04672, USA

    Peter F. Straub

  3. The Wetlands Institute, Stone Harbor, New Jersey, USA

    Peter F. Straub, Mary L. Higham, L. Stanton Hales Jr. & Theodore K. M. Thwing

  4. The Haskins Shellfish Laboratory, Rutgers University, Bivalve, New Jersey, USA

    Arnaud Tanguy & Brenda J. Landau

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  1. Peter F. Straub
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Straub, P.F., Higham, M.L., Tanguy, A. et al. Suppression Subtractive Hybridization cDNA Libraries to Identify Differentially Expressed Genes from Contrasting Fish Habitats. Mar. Biotechnol. 6, 386–399 (2004). https://doi.org/10.1007/s10126-004-3146-6

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