Neil Saunders

Focusing on post-transcriptional regulation of expression by small RNA - Neil Saunders

~ 85 sRNA known from E.coli; targets and function often unknown, but often conserved - Neil Saunders

miRNA regulators in eukaryotes: mechanism still unclear (inhibition/degradation/both) - Neil Saunders

> 500 miRNA in humans; also conserved; also few targets or functions known - Neil Saunders

Comparing sRNA regulation to other types; transcriptional, PPI - Neil Saunders

Modelling and simulation of regulation: regulator may be (1) always expressed, (2) switched on by external signal - Neil Saunders

sRNA regulation advantageous where fast response required - Neil Saunders

Next: how does this integrate with transcriptional regulation? - Neil Saunders

Finally, someone provides a clear, succinct summary of what a network interaction graph is - Neil Saunders

Where 2 TFs required, feed-forward loop = AND gate - Neil Saunders

May be mixed loops: combination of ncRNA and protein factors - Neil Saunders

Example mixed feed-forward loop: OmpR + MicF (sRNA) -> ompF - Neil Saunders

Other examples known in bacteria and human - Neil Saunders

Mixed negative feedback loops: e.g. RyhB -> Fur, E. coli; stochastic simulation. - Neil Saunders

Summary: mixed regulation extends possible regulation dynamics - Neil Saunders

Moving onto predicting miRNA targets in genomes - Neil Saunders

Use known targets to narrow the solution space; miRNA "seed region"; conservation at target site; repeat binding sites - Neil Saunders

RepTar algorithm: starts with 3'-UTR, HMM profiles repetitive signals, matches to miRNAs - Neil Saunders

Validation using shuffled sequences and experimental data; not over-selling the method - Neil Saunders

Predicted miRNAs: seed match (84%), 3'-compensatory (11%), nearly-full match (5%) - Neil Saunders

Moving on to applications of RepTar: viral miRNAs - Neil Saunders

Significant overlap of predicted targets for different viruses: GO annotations make sense - Neil Saunders

Second set of targets are immune system-related; do viruses use miRNA to down-regulate immune system? - Neil Saunders

HCMV: evades NK cells by mimicking MHC-I to make cell appear "self" - Neil Saunders

MICB - top target for HCMV miRNA UL112; experimental validation by over-expressing UL112 in cell lines; MICB down-regulated, controls are not. Also use luciferase reporter assay with 3'-UTR and mutagenesis of binding site. - Neil Saunders

Viral infection of UL112 deletion mutant confirms results - Neil Saunders

Describing further experimental confirmation. Obviously quite excited about her results :) - Neil Saunders

Viral miRNAs may therefore be therapeutic targets; e.g. for antisense RNA, or mimic miRNA effect for immunosuppression - Neil Saunders

Great talk. Wrapping up now - running through almost to 10 am. - Neil Saunders

Good coverage too, Neil - Roland Krause

Wow, the Neil Saunders one-man show :) - Lars Juhl Jensen