The Research Of Analytical Methods Of Virus's Small-RNA Characteristics

With the rapid development of biological science and technology, the accumulation speed of biological data will keep accelerating, which means more demands for scientific analysis methods. Bioinformatics can help us understand the nature of biology, decipher genome information and clarify the relationship of the information more comprehensively. For a large number of nucleic acid and protein, information processing and analysis is needing, through the pretreatment, we can find useful clues, on the basis of which, molecular biology experiments with a clear purpose can be made.Virus research is closely related to life science and technology, because virus is the simplest model on life activity research, and provides much basic information during the process of people understanding the phenomenon of life. In recent years, with the biochip technology development and diffusion, virus nucleotide sequence has been detected easily, however, people know little about the biological characteristics of these sequences. miRNA and siRNA both is small molecule RNAs which have been found in recent years. At present they are considered as an important way of gene self-regulation, and involved in viral infections and transposon silence processes. RNAi in the treatment of viral infectious disease has gained great attention. Therefore, we study the characteristics of the virus on the miRNA and siRNA level, which has important practical significance on the understanding of the mechanism of the virus, as well as the diagnosis and treatment of disease that caused by virus.(1) Association and distinction between miRNA and siRNA. They have similar length, and both have the function of translational repression and mRNA cleavage through sequences complementary. Both from the point of view of genetics and biochemistry are two different ways, but they have some common elements participate in two ways. This suggested that there may be overlapping mechanisms, or to share the same entry site. The classification of miRNA-mRNA target site by Stephen Cohen and his mates has been widely recognized. Based on it, we download the sequences of miRNAs and siRNAs from some authoritative databases like miRBase, select the binding motif from 5'UTR 2-8 sites, find the siRNAs which have possibility of function on the same target, and conclude the category information. In our category, we select the 89 siRNAs which related to oncogenes or tumor suppressor genes, and find that there are 50 target-related miRNAs, among which we have know that some have significantly abnormal expression in the colon and lung cancer cells, such as miR-21, miR-145 and miR-188.Since the miRNAs are only a small part of all that we know the function exactly, we use siRNA to research miRNA will give some help for explaining the phenomenon of life and disease treatment, it will also be conducive to efficient use of cells because miRNAs are endogenesis.(2) miRNA and virus. Some viruses can lead to occurrence of malignant tumors, which always accompanied with the abnormal expression of miRNAs in these tumor cells and proximal organizations. We select two representative types of viruses: human herpesvirus which can lead to cancer and human adenovirus which not lead to cancer. We mark the miRNA target in the virus; collect statistics of the number and frequency in every virus. To observe the results we can find that the two statistics in herpesvirus are higher than adenovirus, the frequency in carcinogenic EBV and CMV are higher than the other herpesvirus. We hypothesize that if virus involve in the cancer signaling pathways, it needs some other miRNAs besides that in virus infection mechanisms.BLAST the virus with mature miRNAs (21-23nt) appears in last step. The target statistics indicate functional association between miRNAs and virus, BLAST is further analysis from the overall level. The high-score match sequences indicate that the miRNAs may be relevant to the miRNAs that generate by virus itself. Also, BLAST results can be used to analyze the virus structure that similar to the hairpin miRNA precursor.(3) siRNA and virus. RNAi is a powerful method in laboratory; we can use it to induce gene silence. SiRNAs play a key role in the RNAi pathways. We choose mature siRNAs that can silent oncogenes and tumor suppressor genes, statistic the target information in every herpesvirus respectively. According to the target we establish association between herpesvirus and oncogenes and tumor suppressor genes. Moreover, we BLAST the oncogenes and tumor suppressor genes associated siRNAs with herpesvirus. From the results, we conclude that the carcinogenic herpesvirus (HSV-1, HSV-2, EBV, CMV) are all relevant to SPHK1 pathway; NFKB2-CTGF-SPHK1-RAF1 (FGFR1-SPI1),NFKB2-CTGF-SPHK1-RAF1-FGFR1-MYC-BRAF,CTGF- SPHK1-RAF1-FGFR1-WNT1-MAPK8 are the key genetic patterns of HSV-1/2, EBV and CMV carcinogenic mechanism. In addition, given the importance of promoter in gene transcription, we compute the space between match items'start position and each promoter; mark the minimal space.(4) Homology viruses. We analyze some carcinogenic viruses, such as EBV, and their homology, to identify the common and individual areas; combine these areas with the results in former chapters. This will help to find the common and individual characteristics of homology viruses.In this paper, the experimental methods can be used for reference in the future related work. The large amounts of data and form information not only can be used to form the follow-up databases establishment, but also play a certain directive role in the design of biological experiments.