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Information Entropy Analysis of Important Sites in microRNA and Computional Prediction of Novel microRNAs and Their Targets in Sorghum(Sorghum Bicolor)

Author: DuJiangFeng
Tutor: TaoShiZuo；WuYongJun
School: Northwest University of Science and Technology
Course: Biochemistry and Molecular Biology
Keywords: microRNA conservative information entropy base correlation sorghum
CLC: S514
Type: Master's thesis
Year: 2009
Downloads: 63
Quote: 1
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Abstract

The work is mainly composed of two aspects. One is on the sites’ conservatism and base correlation of precursor and mature miRNA sequences by the means of informatic entropy; the other is predicting the novel candidate miRNAs and their targets in sorghum by computational method and secondary structure.MicroRNAs (miRNAs), ranging in size from 20 to 25 nucleotides, are a class of endogenous regulatory noncoding RNAs that have been found in various eukaryotes. Mature miRNAs are processed from longer primary transcripts by a series of ribonuclease, and then incorporated into RNA-induced silencing complex (RISC), in which they recognize target mRNA by base-pairing and guide RISC to cleave the mRNA or inhibit the translation of the mRNA, depending on the complementarity between them. Recent advances have revealed that miRNAs participate in a variety of regulatory pathways, including development, virus prevention, hematopoiesis, organogenesis, cell proliferation and apoptosis, fat metabolism, etc.Large number of studies show that precursor does the very important role in miRNA’s maturation. Almost all of precursors have stem- loop shape in the secondary structure and they have relative high minimum free energy (MFE). This study mainly analysed the conservatism of some special sites of precursor miRNAs in primary structure via mathematics method and attempt to find some significant information which are useful for the miRNA biogenesis and prediction of new candidate miRNA through bioinformatics.The results showed that D2(L) have more information than D1(L), though D1(L) changes roughly consistently with the D2(L) in each group. Viral pre-miRNAs are more conservative than those belonging to animals or plants. In addition, U is dominant in most sites compared with other nucleotides. We also found that in the middle of some groups, some sites where miRNAs cut down from pre-miRNAs by Enzyme Dicer are significant conservative.Then we have predicted new candidate miRNAs and their targets in sorghum’s GSS database through computational method. Using a homology search based on genomic survey sequence (GSS) analysis and microRNA (miRNA) secondary structure, a total of 17 new miRNAs were identified. They are distributed unevenly among 11 miRNA families. Some miRNA genes were found in multiple locations and in more than one genomic context. Most miRNAs are conserved within the same kingdom, but we found in Sorghum that sbi-miR127 and sbi-miR466 showed conservation with H. sapiens and M. musculus, respectively. The subjection of those 17 new miRNAs to online software miRU showed that they might regulate 64 target genes, most of which are involved in RNA processing, metabolism, cell cycle, protein degradation, stress response and transportation. At least 7 of 11 miRNA families target NADPH-cytochrome P450 reductase, nucleoside diphosphate kinase, superoxide dismutase, etc., proteins that are necessary in metabolism and stress response, suggesting that miRNAs play an important role in these processes.

Information Entropy Analysis of Important Sites in microRNA and Computional Prediction of Novel microRNAs and Their Targets in Sorghum(Sorghum Bicolor)

Abstract

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