BY m.ghorbani

1. BY m.ghorbani MiRNA in computational biology The Nobel Prize in Physiology or Medicine for 2006 Andrew Z. Fire and Craig C. Mello for their discovery of "RNA interference – gene silencing by double-stranded RNA"

2. Dedicated to all mothersin the world

3. contents • Introduction miRNA • Computational identification of miRNA • Computational identification of target miRNA • miRNA database Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

4. Introduction miRNA • MicroRNA are one class of newly identified riboregulators of gene expression in many eukaryotic organism. • Mature miRNA have 20-24 nucleotides Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

5. Tasks of miRNA • They play important roles in multiple biological and metabolic processes , including • Developmental timing • Signal transduction • Differentiation • Cell fate identity • Diseases and carcinogenesis Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

6.  Coordinated action of miRNA nodes in developmental timing and tailoring leaf shape www.cs.ucf.edu/~shzhang/CAP5510/lec14.ppt

7. Produce mature miRNA • Mature miRNA formation requires a multiple –step process. • miRNA gene is first transcribed to a primary miRNA by Pol II enzyme • Cleaved to a stem loop intermediate termed pre-miRNA by Drosha • Pre-miRNAs are further cleaved to miRNA: miRNA* duplex • Mature miRNA are releaseed for regulating targeted gene expression Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

8. How microRNA regulates the target mRNA genes www.cs.ucf.edu/~shzhang/CAP5510/lec14.ppt

9. Major characterstics of microRNAs • Hairpin-shaped secondary structures • High conservation for some miRNA • High minimal folding free energy index Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

10. History identification of miRNA • miRNAS were initially identified by a genetic screening technology • Recently , direct cloning of miRNAs , followed by small RNA isolation • Computational approaches Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

11. Computational approaches • The principles of computational approaches are base on • Hairpin-shaped stem loop secondary structure • High evolutionary conservation • High minimal folding free energy index Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

12. classification • The computational approaches can be classified into five major categories • Homology search-based • Gene search • Neighbor stem loop search • Algorithms based on comparative genomics • Phylogentic shadowing-based Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

13. Homology search-based approach • Identifying miRNA genes by searching nucleotide database using BLOST program • It was well recognized that miRNA are evolutionarily conserved • Profile-based search programs , such as • ERPIN • miAlign Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

14. Classification of homology s.. • GENOME-BASE SEARCH • ESTS-BASE SEARCH • Partial cDNA sequences of expressed gened cloned into a plasmid • A powerfull approach to identify miRNA genes in species whose genome sequence are not available Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

15. GENE-FINDING APPROACH • Gene-finding approaches are designed for predicting animal miRNA • Not depend on homology or miRNA conservation Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

16. How gene-finding work • First need to identify conserved genomic regions • These regions into a window 110-n • Using a specific computer program Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

17. How program work • Window is folded with secondary structure program such as mfold or RNA fold • hairpin-shaped stem loops for potential miRNA candidates Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

18. Computer programs homology search based • MiRseeker • analyzing conserved sequences that adopt an extended stem loop secondary structure • Accuracy 75% for Drosophila miRNA • miRscan • Identify miRNA base on common characteristics (such as base pairing and nucleotide bias ) Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

19. MiRscan • Scan to find conserve hairpin structures • Using known miRNA genes at training set Yong Huang. The discovery approaches and detection methods of microRNAs

20. Processes of MiRscan • A 110-nt window along both strand • Folding the window with RNAfold • A folding free energy of as a least -25 kcal/mol • Passing a 21-nt window along each stem-loop • Assigning a log likelihood score to each position for its similarity to know miRNA Yong Huang. The discovery approaches and detection methods of microRNAs

21. Program online http://bioinforma.weebly.com/mirna-prediction.html

22. MiRscan http://bioinforma.weebly.com/mirna-prediction.html

23. Computational identification of microRNA TARGETS • A high degree of complementarity to the miRNAs • This allows the prediction of miRNA targets by computational approaches Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

24. Computational approaches are based on • MiRNA are perfectly or near perfectly complementary to their target miRNA • The RNA-RNA duplex has a higher negative folding free energy • Binding sites of mRNA and miRNA is highly conserved Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

25. programs • Find miRNA • Mir check • Target scan • MiRanda Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

26. miRNA database • miR Base • ASRP • miRnaAMap Boahongzhang ,xiaoping pan , 2006. computational identification of miroRNA

27. THANK YOU END