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miRNA Background & Bioinformatics

miRNA Background & Bioinformatics. Seungyoon Nam. RNA World. Bioinformatics Seminar, By Yaron Levy. What’s in a Name?. small RNAs. The Nobel Prize in Physiology or Medicine 2006. "for their discovery of RNA interference - gene silencing by double-stranded RNA". Craig C. Mello

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miRNA Background & Bioinformatics

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  1. miRNABackground & Bioinformatics • Seungyoon Nam

  2. RNA World Bioinformatics Seminar, By Yaron Levy

  3. What’s in a Name?

  4. small RNAs

  5. The Nobel Prize in Physiology or Medicine 2006 "for their discovery of RNA interference - gene silencing by double-stranded RNA" Craig C. Mello University of Massachusettsl Andrew Z. Fire Stanford University From Prof. Shin’s informal lecture at Stanford 2008.

  6. RNAi : siRNA

  7. Milestones in miRNA research

  8. miRNA vs siRNA

  9. miRNA : Discovery • lin-4 in C.elegans • first known to control the timing of C.elegans larval development. • does not code for a protein. • two species:small one 22 nt in length (mature miRNA), large one 61 nt in length (pre-miRNA). • antisense complementarity to multiple sites in the 3’ UTR of the lin-14. • reduces the amount of LIN-14 protein without noticeable change in levels of lin-14 mRNA.

  10. microRNA • MicroRNAs are a family of small non-coding RNAs 18-22 in length that regulate gene expression in a sequence-specific manner. • microRNAs have been discovered in animals and plants, where the number of miRNAs is expected to 500-1000 per species. • Nearly all miRNAs are conserved in related species and many of them have homologs in distant species. • Also, microRNAs have been found in viruses such as Epstein-Barr virus, Kaposi sarcoma-associated herpesvirus and etc.

  11. First miRNA in C.elegans miRNA in Plants miRNA in C.elegans with homologs In flies and human

  12. miRNA : Biogenesis

  13. miRNA : Biogenesis Posttranscriptional regulation Direct cleavage

  14. Distribution of Mammalian miRNAs Found in Introns and Exons of Host Transcripts

  15. Pri-miRNA structure

  16. A model for the processing of intronic microRNA

  17. The pri-miRNA boundary

  18. Processing of pri-miRNA

  19. miRNA-mRNA Interaction

  20. It’s not at all

  21. Expression of miRNA

  22. miRNA function (posttranscriptional regulation)

  23. miRNA: Function MiRNA mediated repression is affected by certain circustances. miR-122 miR-134

  24. miRNA and Disease Blue bar: miRNA

  25. miRNA and disease

  26. miRNA & cancer

  27. Database for miRNA

  28. Databases for miRNA

  29. Databases for miRNA From Prof. Shin’s informal lecture at Stanford 2008.

  30. Databases for miRNA

  31. Computational miRNA Gene & Target Finding

  32. Computational identification of microRNA targets • Three major characteristic properties • MiRNAs are perfectly or near-perfectly complementary to their target mRNAs. • Although the complementarity between miRNAs and their targets were not perfect in animals, there still are some 5’ 7-9 nt seed regions between them. • The miRNA-mRNA duplex has a lower folding free energy. • Mature miRNAs, binding sites of mRNA to miRNA, and miRNA:mRNA duplex are highly conserved from species to species. Computational Biology and Chemistry 30,395–407 (2006)

  33. Computational identification of microRNA targets

  34. New breakthrough

  35. Potent effect of target structure on microRNA function. For multiple sites in a UTR.

  36. Potent effect of target structure on microRNA function. Only hybridization considered Real experiment Their result

  37. The role of site accessibility in microRNA target recognition

  38. The role of site accessibility in microRNA target recognition C ( genetically modified ~200bp construct to force it into highly paired (closed ) closed strucuter UTR N ( ~200 bp spanning miRNA target site and its neighborhood)

  39. The role of site accessibility in microRNA target recognition

  40. The role of site accessibility in microRNA target recognition

  41. The role of site accessibility in microRNA target recognition

  42. mirWIP: microRNA target predicition based on microRNA-contataing ribonucleoprotein-containing ribonucleoprotein-enriched transcripts Non-AIN-IP targets AIN-IP targets Comparison (seed pairing, accessibility, energy:S, A, E) Score system

  43. mirWIP: microRNA target predicition based on microRNA-contataing ribonucleoprotein-containing ribonucleoprotein-enriched transcripts

  44. Proteomics joins the search for microRNA targets-Proteome analysis Measuring target protein expression change using SILAC (Stable isotope labelling with amino acids in cell culture) http://en.wikipedia.org/wiki/Image:Silac.gif

  45. Proteomics joins the search for microRNA targets-proteome analysis • mRNA expression change results in proteome expression decreased. • But a specific miRNA controlled proteome expression significantly by translation repression. • It implies translational repression has been underestimated in miRNA regulation.

  46. Proteomics joins the search for microRNA targets-proteome analysis • Ectopic expression or overexpression of miRNAs might not produce the same effects as endogeneous miRNAs. • Blocking let-7b results in upregulated genes in Hela cells that would have down regulated on overexpression.

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