The Difference Analysis Of MicroRNA Regulation In Housekeeping And Non-housekeeping Human Genes And The Thermodynamic Research Of Oligonucleotide Binding Sites

The organism is a multi-level complex system that can self-regulate and execute variousbiological functions through the interactions between molecules in vivo. This paperfocuses on the interactions between oligonucleotides and tries to reveal the internalrules behind the gene expression regulation.MicroRNA (miRNA) is a kind of19-24nt long endogenous non-coding RNA ineukaryote, which can regulate target genes finely at post-transcription level withspecific expressions of tissue, space and time. A number of studies have suggested thatmiRNA plays an important role in many biological processes, such as cell proliferation,differentiation, development, apoptosis and disease development, and its dysfunctioncan lead to multiple human complex diseases such as cancer, cardiovascular. Meanwhilehousekeeping genes are indispensable to maintain cell basic structure and metabolicfunction, and to ensure cell survival and growth. Yet miRNA, an important factor inpost-transcription regulation of genes and degradation of mRNAs, provides another wayfor better understanding the roles of housekeeping genes in biological process. However,there are few systematic studies to discuss the miRNA regulation in housekeeping genes.As a result, we have done the first part of the work:We did the difference analysis of miRNA regulation in housekeeping andnon-housekeeping human genes. We studied the miRNA regulation on the expressionof housekeeping and non-housekeeping human genes from the systemic level, throughthe integration analysis of three sequence-based target gene prediction softwares and theconjoint analysis based on miRNA-targets gene expression information. We also usedphastCons-score based evolution analysis to reveal the influence of conservation at3’UTRs region for the density difference of miRNA regulatory between the two classesof genes. The results showed that housekeeping genes have a significantly higher density of miRNA binding sites and their3’UTR are more conservative. These findingshighlight the importance of miRNA regulation in housekeeping genes, suggesting thatinvestigating the roles of miRNAs on the robustness of housekeeping genes expressionis highly necessary.In the first part, we found that industry methods of miRNA binding sites predictionhave some limits，so other molecular biological technologies based on oligonucleotidehybridization do, such as PCR and gene chip. They use the sequence similarityinformation to predict the oligonucleotide potential binding sites. However, thehybridization reaction between the oligonucleotide and target genes is a thermodynamicprocess. The sequence similarity analysis method such as BLAST could not accuratelyreflect the thermodynamic procedure of oligonucleotide binding. Therefore, we havedone the second part of the work:We developed a program named ThermoMatch to predict the potentialbinding sites of oligonucleotide in genome-wide level based on thermodynamics.ThermoMatch adopted the index algorithm and a divide and conquer strategy to searchall hybrid patterns including match, mismatch and gap structures by thermodynamicsnot sequence similarity against a whole genome background, thus to imitate thehybridization process between oligonucleotide molecules and target genes in vivo.ThermoMatch acts as a comprehensive thermodynamic stability prediction program tohelp user design high quality oligonucleotides, and it will be beneficial for the designand application of chip-based probes, PCR primers, miRNAs and siRNAs in the future.