Whole Genome Search of Candidate Hypoxia Response Genes by Bioinformatic Methodology

• Main Authors: Ko-Fan Chen, 陳克帆
• Other Authors: Shaw-Senq Tsai
• Format: Others
• Language: en_US
• Published: 2005
• Online Access: http://ndltd.ncl.edu.tw/handle/70822334854372391625

碩士 === 國立成功大學 === 生理學研究所 === 93 === Hypoxia is the reduction of environmental oxygen In absent of oxygen, hypoxia inducible factor-1 a (HIF-1a) dimerizes with HIF-1b and binds to the hypoxia response element (HRE) on the target DNA sequence. HIF-1a regulated genes have been found to be involved in cell proliferation, angiogenesis, glycolysis, apoptosis, and tumor formation. The HRE with a short core sequence “RCGTG” is necessary but not sufficient to be bound by HIF-1a. The flanking region also determines the binding activity. Accordingly, the 20 well known HREs were retrieved, aligned, and built up a hidden Markov model based HRE profile. The HMM-based HRE profile was used to search candidate HRE on the promoter region of human and mouse genes. 8170 human genes and 6477 mouse genes were identified by the cutoff score -1.8. About one-third of putative these HIF-1a regulated genes are conserved between human and mouse genome. The expression profiles of randomly picked fifty genes were investigated at various time points after DFO mimic hypoxia treatment. The regulation rate of the genes with positive score is 91%. This indicates that about 2500 human genes and 1600 mouse genes could be regulated by HIF-1a. In analysis of regulation pattern the candidate genes were regulated consistently among different cells or were specifically expressed and/ or regulated in one cell. For the time course analysis, the genes regulated by hypoxia can be further classified into one of early, delay, or biphasic category. The regulation patterns are similar in hypoxia and DFO treatment suggesting that DFO is a proper hypoxia mimetic. By detecting intra nuclear HIF-1a protein and in vivo binding of HIF-1a on the candidate HRE, it was demonstrated the altered RNA expression in candidate genes under chemical or true hypoxia is correlated with nuclear HIF-1a protein level and the binding activity. Put all together, this study demonstrated a high throughput screening and verification approach in understanding the whole picture of gene regulation mediated by hypoxia.