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.