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Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis
Open accessAbstract
Hypoxia is important in both biomedical and environmental contexts and necessitates rapid adaptive changes in metabolic organization. Mammals, as air breathers, have a limited capacity to withstand sustained exposure to hypoxia. By contrast, some aquatic animals, such as certain fishes, are routinely exposed and resistant to severe environmental hypoxia. Understanding the changes in gene expression in fishes exposed to hypoxic stress could reveal novel mechanisms of tolerance that may shed new light on hypoxia and ischemia in higher vertebrates. Using cDNA microarrays, we have studied gene expression in a hypoxia-tolerant burrow-dwelling goby fish, Gillichthys mirabilis. We show that a coherent picture of a complex transcriptional response can be generated for a nonmodel organism for which sequence data were unavailable. We demonstrate that: ( i ) although certain shifts in gene expression mirror changes in mammals, novel genes are differentially expressed in fish; and ( ii ) tissue-specific patterns of expression reflect the different metabolic roles of tissues during hypoxia.
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“For example, genes with the Hig_1_n (PF04588.6 in Pfam) domain were highly expressed under hypoxic stress 22,23”
From The yak genome and adaptation to life at high altitude (2012) · cites this paper as [22]
Citations
Cites
Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction
Chomczynski, P., & Sacchi, N. (1987) · Analytical Biochemistry · doi:10.1006/abio.1987.9999 · Cited by 65,515
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., et al. (2000) · Nature · doi:10.1038/35000501 · Cited by 9,925
Targeting Hypoxia-Inducible Factors for the Treatment of Anemia in Chronic Kidney Disease Patients
Locatelli, F., Fishbane, S. N., Block, G. A., & Macdougall, I. C. (2017) · American Journal of Nephrology · doi:10.1159/000455166 · Cited by 4,836
Diatchenko, L. B., Lau, Y. C., Campbell, A. P., Chenchik, A. A., Moqadam, F., Huang, B. C. B., Lukyanov, S., Lukyanov, K. A., Gurskaya, N. G., Sverdlov, E. D., et al. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.12.6025 · Cited by 3,009
Exploring the new world of the genome with DNA microarrays
Brown, P. O., & Botstein, D. (1999) · Nature Genetics · doi:10.1038/4462 · Cited by 2,430
Systematic variation in gene expression patterns in human cancer cell lines
Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., et al. (2000) · Nature Genetics · doi:10.1038/73432 · Cited by 2,088
Regulation of Mammalian O 2 Homeostasis by Hypoxia-Inducible Factor 1
Semenza, G. L. (1999) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.15.1.551 · Cited by 1,914
Transcriptional regulation of genes encoding glycolytic enzymes by hypoxia-inducible factor 1.
Semenza, G., Roth, P. H., Fang, H. M., & Wang, G. L. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31580-6 · Cited by 1,892
HIF-1: mediator of physiological and pathophysiological responses to hypoxia
Semenza, G. L. (2000) · Journal of Applied Physiology · doi:10.1152/jappl.2000.88.4.1474 · Cited by 1,822
Hochachka, P. W., Buck, L. T., Doll, C. J., & Land, S. C. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.18.9493 · Cited by 1,109
[12] DNA arrays for analysis of gene expression
Eisen, M. B., & Brown, P. O. (1999) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(99)03014-1 · Cited by 1,043
Genome-wide expression monitoring in Saccharomyces cerevisiae
Wodicka, L. M., Dong, H., Mittmann, M., Ho, M.-H., & Lockhart, D. J. (1997) · Nature Biotechnology · doi:10.1038/nbt1297-1359 · Cited by 973
Lee, P. J., Jiang, B.-H., Chin, B. Y., Iyer, N. V., Alam, J., Semenza, G. L., & Choi, A. K. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.9.5375 · Cited by 782
Oxidative stress and heat shock induce a human gene encoding a protein-tyrosine phosphatase
Keyse, S. M., & Emslie, E. (1992) · Nature · doi:10.1038/359644a0 · Cited by 633
Normalization and subtraction: two approaches to facilitate gene discovery.Preprint
Bonaldo, M. F., Lennon, G., & Soares, M. B. (1996) · Genome Research · doi:10.1101/gr.6.9.791 · Cited by 527
Oxygen-regulated transferrin expression is mediated by hypoxia-inducible factor-1
Rolfs, A., Kvietikova, I., Gassmann, M., & Wenger, R. H. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.32.20055 · Cited by 401
Diatchenko, L. B., Lukyanov, S., Lau, Y. C., & Siebert, P. D. (1999) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(99)03022-0 · Cited by 393
Tazuke, S. I., Mazure, N. M., Sugawara, J., Carland, G., Faessen, G. H., Suen, L.-F., Irwin, J. C., Powell, D. R., Giaccia, A. J., & Giudice, L. C. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.17.10188 · Cited by 222
Tob, a novel protein that interacts with p185erbB2, is associated with anti-proliferative activity.
Matsuda, S., Kawamura-Tsuzuku, J., Ohsugi, M., Yoshida, M., Emi, M., Nakamura, Y., Onda, M., Yoshida, Y., Nishiyama, A., & Yamamoto, T. (1996) · PubMed · Cited by 195
Surviving hypoxia without really dying
Boutilier, R. G., & St‐Pierre, J. (2000) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/s1095-6433(00)00234-8 · Cited by 160
Tissue-specific changes in protein synthesis rates in vivo during anoxia in crucian carp
Smith, R. W., Houlihan, D. F., Nilsson, G., & Brechin, J. (1996) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.1996.271.4.r897 · Cited by 133
A central control for cell growth
Whitmarsh, A. J., & Davis, R. J. (2000) · Nature · doi:10.1038/35002220 · Cited by 115
Insulin-like growth factors and their binding proteins in normal and abnormal human fetal growth.
Chard, T. (1994) · PubMed · Cited by 112
The hybridoma revolution: an offshoot of basic research
Milstein, C. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199911)21:11 · Cited by 97
Overexpression of Multisubunit Replication Factors in Yeast
Burgers, P. (1999) · Methods · doi:10.1006/meth.1999.0796 · Cited by 74
Tissue-Specific Controls on Carbohydrate Catabolism during Anoxia in Goldfish
Storey, K. B. (1987) · Physiological Zoology · doi:10.1086/physzool.60.5.30156134 · Cited by 56
Kim, Y. W., Otterson, G. A., Kratzke, R. A., Coxon, A. B., & Kaye, F. J. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.11.7256 · Cited by 45
Gobies of the Genus Gillichthys, with Comments on the Sensory Canals as a Taxonomic Tool
Barlow, G. W. (1961) · Copeia · doi:10.2307/1439585 · Cited by 40
Tumor suppressor proteins as regulators of cell differentiation.
Li, Z., Hromchak, R., Mudipalli, A., & Bloch, A. (1998) · PubMed · Cited by 28
The use of extracellular lactate as an oxidative substrate in the oxygen-limited frog
Donohoe, P., & Boutilier, R. G. (1999) · Respiration Physiology · doi:10.1016/s0034-5687(99)00036-5 · Cited by 19
Isolation of Full-Length cDNA Clones Using SMART TM cDNA and a Biotin-Streptavidin Bead System
Ciavatta, V. T., & Cairney, J. (2000) · BioTechniques · doi:10.2144/00293bm08 · Cited by 9
Research works printed but not linked: 6
- Z R Li, R Hromchak, A Mudipalli, A Bloch Cancer Res 58, 4282–4287 (1998).
- T Chard Growth Regul 4, 91–100 (1994).
- S Matsuda, J Kawamura-Tsuzuku, M Ohsugi, M Yoshida, M Emi, Y Nakamura, M Onda, Y Yoshida, A Nishiyama, T Yamamoto Oncogene 12, 705–713 (1996).
- Y W Kim, G A Otterson, R A Kratzke, A B Coxon, F J Kaye Mol Cell Biol 14, 7256–7264 (1994).
- R W Smith, D F Houlihan, G E Nilsson, J G Brechin Am J Physiol 271, R897–R904 (1996).
- N M Aguilar Ph.D. thesis (Scripps Oceanographic Institute, Univ. of California, San Diego), pp. 201 (2000).
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Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2343 · Cited by 983
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Somero, G. N. (2002) · Integrative and Comparative Biology · doi:10.1093/icb/42.4.780 · Cited by 899
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Wu, R. S. S. (2002) · Marine Pollution Bulletin · doi:10.1016/s0025-326x(02)00061-9 · Cited by 836
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Wood, A. W., Duan, C., & Bern, H. A. (2005) · International Review of Cytology · doi:10.1016/s0074-7696(05)43004-1 · Cited by 657
Metadata
- Authors
- Gracey, A. Y., Troll, J. V., & Somero, G. N.
- Affiliations
- Hopkins Marine Station (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2001-02-13
- Volume
- 98
- Issue
- 4
- Pages
- 1993-1998
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC29370
- OpenAlex
- W2008308093
- Cited by
- 561
- References
- 32
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 15 · 2023: 9 · 2022: 10 · 2021: 21 · 2020: 13 · 2019: 18 · 2018: 20 · 2017: 31 · 2016: 21 · 2015: 19 · 2014: 19 · 2013: 23 · 2012: 21
- FWCI
- 27.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Environmental Science › Ecology › Physiological and biochemical adaptations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant responses to water stress
- Keywords
- hypoxia, hypoxia tolerance, Gillichthys mirabilis, gene expression profiling, transcriptional response, tissue-specific gene expression, hypoxia-ischemia
- MeSH terms
- Amino Acids, Animals, Hypoxia, Base Sequence, Brain, Cell Division, Glycolysis, Liver, Molecular Sequence Data, Myocardium, Oxygen, Perciformes, DNA, Complementary, Muscle, Skeletal, Gene Expression Profiling
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