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MicroARNs, comparaison, prediction

MicroARNs, comparaison, prediction. Eric Bonnet Bioinformatics & Evolutionary Genomics Department of Plant Systems Biology Ghent University / VIB Belgium. Small RNAs biogenesis and function. Plan de la presentation. But de la presentation

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MicroARNs, comparaison, prediction

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  1. MicroARNs, comparaison, prediction Eric Bonnet Bioinformatics & Evolutionary Genomics Department of Plant Systems Biology Ghent University / VIB Belgium

  2. Small RNAs biogenesis and function

  3. Plan de la presentation • But de la presentation • Biogenese, fonction et prediction des petits ARN non-codants. • Plan de la presentation • 1/ Biogenese et fonction des petits ARN non-codants • 2/ Principes de prediction bioinformatique des microARN

  4. Tiling arrays • Tiling arrays: using probes to analyze expression of complete genomic regions. => transcriptome (a lot) bigger than expected. => many non coding RNAs

  5. Non coding RNAs classes • Degradation products • Ribosomal RNA • Transfer RNA • Small nucleolar RNA • … • microRNA (miRNA) • Short interfering RNA (siRNAs)

  6. Small RNAs • Very short: ~21 nt • Discovered (very) recently (1993) • Regulate expression of protein coding genes at the post-transcriptional level • “Dark matter” of Biology

  7. Small RNA biogenesis

  8. miRNA versus siRNA • miRNA: • Processed from imperfect stem-loop hairpin-like structures. • Encoded by independent loci. • siRNA • Processed from long double stranded RNA sequences. • Regulate the genes from which they originate.

  9. miRNA biogenesis

  10. siRNA biogenesis

  11. miRNA / siRNA functions • Regulation of gene expression [miRNA] • Defense against exogenous sequences (viruses, pathogens, etc..). [siRNA] • Chromatin structure: siRNA mediates silencing of Tranposons, transgenes at the DNA level (methylation). [siRNA]

  12. miRNA function in animals

  13. ???

  14. miRNA function in plants

  15. miRNA gene prediction

  16. miRNA computational prediction = ?

  17. Solution: filtering • Reduce false positives using: • Structural & compositional features • Comparative genomics • Statistical properties

  18. Structural & compositional features MiRNA is part of one continuous helix Unpaired bases miRNA: max 5 & Maximum bulge size: 2 G.U pairs: maximum 5 Unpaired bases miRNA*: max 5 Paired bases : minimum 15 Free energy: maximum -30 Kcal/mol MiRNA GC content & entropy value

  19. Comparative genomics

  20. Permutation test: Compare Free energy value for a miRNA precursor with the value of re-shuffled sequences. Precursor statistical properties

  21. miRNA gene prediction in plants

  22. miRNA genes prediction in animals

  23. What’s the catch ? • => Evidence for miRNA genes not conserved in other organisms (specific). • => Comparative genomics filter can not be used • => Use RNA high-throughput expression data (MPSS, “454”) to check predictions.

  24. miRNA targets prediction

  25. Future

  26. Bibliography Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004 Jan 23;116(2):281-97. Baulcombe D. RNA silencing in plants.Nature. 2004 Sep 16;431(7006):356-63. Bonnet E, Van de Peer Y, Rouze P. The small RNA world of plants.New Phytol. 2006;171(3):451-68.

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