Download Discovering plant MicroRNAs: lessons from comparative

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
– Biogenese, fonction et prediction des petits ARN
non-codants.
• Plan de la presentation
– 1/ Biogenese et fonction des petits ARN noncodants
– 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
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
Comparative genomics
Precursor statistical properties
• Permutation test:
– Compare Free energy value for a miRNA precursor with the value
of re-shuffled sequences.
1a
150
50
100
Number of sequences
200
250
250
200
150
100
50
0
0
Number of sequences
C. Elegans - tRNA39
1b
C. Elegans - let7 miRNA
-45
-40
-35
-30
-25
-20
Minimum free energy value
-15
-35
-30
-25
Minimum free energy value
-20
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.