Regular Group Meeting Cheung Kwan Yau , Donald 26 th July, 2012

1. Regular Group Meeting Cheung Kwan Yau, Donald 26th July, 2012

2. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Outline • Background • Motivation • Dataset • Methods • Results • Improve the specificity of the target predictions • Conclusion and Discussion

3. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Background • Non-coding RNAs • RNA that do not translate into protein • i.e. miRNA, siRNA, sRNA, … • Biological Functions • Translation • RNA splicing • Gene regulation • … • RNA-RNA interaction Image credit: http://www.dna-sequencing-service.com/dna-sequencing/dna-rna-protein/

4. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Background • sRNAs • small regulatory RNAs in bacteria • functional analogs to miRNAs • different in size and structure (Typically 50–250 nt) • Knowledge about sRNA-mRNA interactions • Involves a core interaction of six to eight contiguous base pairs • Typically utilize well-accessible regions MicF RNA Image Credit: Wikipedia http://en.wikipedia.org/wiki/MicF_RNA

5. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Motivation • Computational approaches for RNA-RNA interaction predictions have high false positive rate • Little investigationhas been made on features associated with the binding sites of mRNAs that are targeted by sRNAs • Explore whether the accessibility and conservation are general features of in the interaction sites in sRNA and targets mRNAs

6. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Dataset – Accessibility analysis • Positive dataset • 74 experimental validated sRNA-mRNA interactions from E. coli and Salmonella • Negative dataset • Predicted by IntaRNA • Selected the putative candidates with similar features with different sequences

7. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Dataset – Conservation analysis • sRNAs and mRNAs sequences from 21 enterobacterialspecies from NCBI RefSeq database

8. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Method – Accessibility • Accessibility • Probability that nucleotides si…sjin an RNA sequence s are unpaired (PU) • Expected fraction of unpaired bases of a subsequence sa…sb(EF)

9. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Method – Conservation • Conservation • Information content Iiof an alignment column Ai • Sequence conservation Ca,bof consecutive alignment columns from Aato Ab

10. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Accessibility • sRNAs and mRNAs interaction sites are significantly accessible • Significant p-value in Wilcoxon rank sum test

11. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Accessibility

12. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Accessibility • Study accessibility of perfectly matching sub-interactions

13. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Conservation • Conserved in the sRNAs interaction sites but not target interaction sites

14. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Conservation • Interactions between sRNAs and targets are not structurally conserved in general

15. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Sequence Composition • More ‘U’ in sRNAs sequences • More ‘A’ and less ‘G’ in target sequences

16. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Base Pairing Conservation • RyhBsRNA sequence conserved in 19 out of 21 species • Base pairing conservation varies

17. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results – Base Pairing Conservation • RybBsRNA sequence conserved in 21 out of 21 species • Base pairing conservation varies

18. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Results - Summary • Both sRNA and target are highly accessible • The sRNA binding region show high sequence conservation • True sRNA binding sites have more ‘U’ • True target binding sites have more ‘A’ but less ‘G’

19. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Improve the specificity of target predictions • Two Strategy • Identify regions of sRNAs and targets which is highly accessible • Identify conserved and weakly structured regions in sRNAs • Improve IntaRNA • Allow the interaction in PU* greater than the q-quantile of the background PU* • Utilize the sequence-structure alignment computed from LocaRNA-P

20. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Improve the specificity of target predictions • Genome Wide Prediction for every sRNA with and without constraints • The constraints improve the performance

21. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Conclusion • Find some general features from the limited data • Apply some constraints to their programs IntaRNA to improve the specificity

22. Accessibility and conservation General features of bacterial small RNA-mRNA interactions? Discussion • Generalization? • Why the target binding sites do not conserved?