Browse > Article
http://dx.doi.org/10.15433/ksmb.2015.7.2.035

Prediction of Hypoxia-inducible Factor Binding Site in Whale Genome and Analysis of Target Genes Regulated by Predicted Sites  

Yim, Hyung-Soon (Korea Institute of Ocean Science & Technology)
Lee, Jae-Hak (Korea Institute of Ocean Science & Technology)
Publication Information
Journal of Marine Bioscience and Biotechnology / v.7, no.2, 2015 , pp. 35-41 More about this Journal
Abstract
Whales are marine mammals that are fully adapted to aquatic environment. Whales breathe by lungs so they require adaptive system to low oxygen concentration (hypoxia) while deep and prolonged diving. However, the study for the molecular mechanism underlying cetacean adaptation to hypoxia has been limited. Hypoxia-inducible factor (HIF) is the central transcription factor that regulates hypoxia-related gene expression. Here we identified HIF-binding sites in whale genome by phylogenetic footprinting and analyzed HIF-target genes to understand how whales cope with hypoxia. By comparison with the HIF-target genes of terrestrial mammals, it was suggested that whales may retain unique adaptation mechanisms to hypoxia.
Keywords
whale; hypoxia; HIF (hypoxia-inducible factor); HIF-target gene; adaptation mechanism;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Crighton, D., Wilkinson, S., O'Prey, J., Syed, N., Smith, P., Harrison, P..R, Gasco, M., Garrone, O., Crook, T. and Ryan, K. M. 2006. DRAM, a p53-induced modulator of autophagy, is critical for apoptosis. Cell, 126, 121-134.   DOI
2 Elnitski, L., Jin, V. X., Farnham, P. J. and Jones, S. J. 2006. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 16, 1455-1464.   DOI
3 Feliubadalo, L., Arbones, M. L., Manas, S., Chillaron, J., Visa, J., Rodes, M., Rousaud, F., Zorzano, A., Palacin, M. and Nunes, V. 2003. Slc7a9-deficient mice develop cystinuria non-I and cystine urolithiasis. Hum. Mol. Genet. 12, 2097-2108.   DOI
4 Goodyer, P., Boutros, M. and Rozen, R. 2000. The molecular basis of cystinuria: an update. Exp. Nephrol. 8, 123-127.   DOI
5 Hochachka, P. W., Owen, T. G., Allen, J. F. and Whittow, G. C. 1975. Multiple end products of anaerobiosis in diving vertebrates. Comp. Biochem. Physiol. B. 50, 17-22.   DOI
6 Lee, J., Giordano, S. and Zhang, J. 2012. Autophagy, mitochondria and oxidative stress: cross-talk and redox signalling. Biochem. J. 441 523-540.   DOI
7 Mirceta S., Signore A.V., Burns J.M., Cossins A.R., Campbell K.L. and Berenbrink M. 2013. Evolution of mammalian diving capacity traced by myoglobin net surface charge. Science. 340, 1234192. doi:10.1126/science.1234192.   DOI
8 Ortiz-Barahona, A., Villar, D., Pescador, N., Amigo, J. and del Peso, L. 2010. Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription- profiling data and in silico binding site prediction. Nucleic Acids Res. 38, 2332-2345.   DOI
9 Potthoff, M. J. and Olson, E. N. 2007. MEF2: a central regulator of diverse developmental programs. Development. 134, 4131-4140.   DOI
10 Semenza, G. L. 2012. Hypoxia-inducible factors in physiology and medicine. Cell. 148, 399-408.   DOI
11 Thewissen, J.G.M., Cooper, L.N., Clementz, M.T., Bajpai, S. and Tiwari, B.N. 2007. Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature. 450, 1190-1194.   DOI
12 Watwood, S. L., Miller, P. J. O., Johnson, M., Madsen, P. T. and Tyack.P. L..2006. Deep-diving foraging behaviour of sperm whales (Physeter macrocephalus). J. Anim. Ecol. 75, 814-825.   DOI
13 Thompson, W., Conlan, S., McCue, L. A. and Lawrence, C. E. 2007. Using the Gibbs Motif Sampler for phylogenetic footprinting. Methods Mol. Biol. 395, 403-424.   DOI
14 Tonjes, A. and Kovacs, P. 2013. SGLT2: a potential target for the pharmacogenetics of Type 2 diabetes? Pharmacogenomics. 14, 825-833.   DOI
15 Vallon, V., Platt, K. A., Cunard, R., Schroth, J., Whaley, J., Thomson, S. C., Koepsell, H. and Rieg, T. 2011. SGLT2 mediates glucose reabsorption in the early proximal tubule. J. Am. Soc. Nephrol. 22, 104-112.   DOI
16 Wenger, R. H., Stiehl, D. P., and Camenisch, G. 2005. Integration of oxygen signaling at the consensus HRE. Sci STKE. 2005, re12.
17 Wittenberg J. B. 1970. Myoglobin-facilitated oxygen diffusion: role of myoglobin in oxygen entry into muscle. Physiol Rev. 50, 559-636.   DOI
18 Yim H. S., Cho, Y.S., Guang, X., Kang, S. G., Jeong, J. Y., Cha, S. S., Oh, H. M., Lee, J. H., Yang, E. C., Kwon, K. K., Kim, Y. J., Kim, T. W., Kim, W., Jeon J. H., Kim, S. J., Choi, D. H., Jho, S., Kim, H. M., Ko, J., Kim, H., Shin, Y. A., Jung, H. J., Zheng, Y., Wang, Z., Chen, Y., Chen, M., Jiang, A., Li, E., Zhang, S., Hou, H., Kim, T. H., Yu, L., Liu, S., Ahn, K., Cooper, J., Park, S. G., Hong, C. P., Jin, W., Kim, H. S., Park, C., Lee, K., Chun, S., Morin, P. A., O'Brien, S. J., Lee, H., Kimura, J., Moon, D. Y., Manica, A., Edwards, J., Kim, B. C., Kim, S., Wang, J., Bhak, J., Lee, H. S. and Lee, J. H. 2014. Minke whale genome and aquatic adaptation in cetaceans. Nat. Genet. 46, 88-92   DOI