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

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Presentation on theme: "MicroARNs, comparaison, prediction Eric Bonnet Bioinformatics & Evolutionary Genomics Department of Plant Systems Biology Ghent University / VIB Belgium."— Presentation transcript:

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

12 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]

13 miRNA function in animals

14 ???

15 miRNA function in plants

16 miRNA gene prediction

17 miRNA computational prediction = ?

18 Solution: filtering Reduce false positives using: –Structural & compositional features –Comparative genomics –Statistical properties

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

20 Comparative genomics

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

22 miRNA gene prediction in plants

23 miRNA genes prediction in animals

24 Whats 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.

25 miRNA targets prediction

26 Future

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


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