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MicroARNs, comparaison, prediction
Eric BonnetBioinformatics & Evolutionary GenomicsDepartment of Plant Systems BiologyGhent University / VIBBelgium
Small RNAs biogenesis and function
Plan de la presentationB ut de la presentation
B iogenese, fonction et prediction des petits A R N non-codants.
Plan de la presentation
1/ B iogenese et fonction des petits A R N non-codants
2 / Principes de prediction bioinform atique des m icroA R N
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
Tiling arrays
• Tiling arrays: using probes to analyze expression of complete genomic regions.
=> transcriptome (a lot) bigger than expected.
=> many non coding RNAs
Non coding RNAs classes
– Degradation products– Ribosomal RNA– Transfer RNA– Small nucleolar RNA– …– microRNA (miRNA)– Short interfering RNA (siRNAs)
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
Small RNA biogenesis
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.
miRNA biogenesis
siRNA biogenesis
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]
miRNA function in animals
???
miRNA function in plants
miRNA gene prediction
miRNA computational prediction
=
?
Solution: filtering
• Reduce false positives using:– Structural & compositional features– Comparative genomics– Statistical properties
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
Comparative genomics
Precursor statistical properties
• Permutation test:– Compare Free energy value for a miRNA precursor with the
value of re-shuffled sequences.
C. Elegans - let7 miRNA
Minimum free energy value
Numb
er of
sequ
ence
s
-45 -40 -35 -30 -25 -20 -15
050
100
150
200
250
1aC. Elegans - tRNA39
-35 -30 -25 -20
050
100
150
200
250
1b
Numb
er of
sequ
ence
s
Minimum free energy value
miRNA gene prediction in plants
miRNA genes prediction in animals
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.
miRNA targets prediction
Future
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.