1. A turbo intro to (the bioinformatics of) microRNAs 11/6 2009 Peter Hagedorn

2. Discovery of microRNA The first described microRNA, lin-4, was cloned and characterised as a translational repressor of developmental timing from C. elegans by Lee et al (1993) and Wightman et al (1993). The transcript of this gene was highly unusual as it was non-coding, and produced extremely small transcripts (22nt) from hairpin structured RNA precursors. Second microRNA, let-7, was also cloned from C. elegans (Reinhart et al, 2000).

3. microRNA research 1600 1400 1200 1000 800 600 400 200 0 2001 2002 2003 2004 2005 2006 2007 2008 Time (year) Number of publications microRNAs discovered in human, mice, and Drosophila microRNAs implicated in leukemia microRNAs identified in viral genomes Drugs against microRNAs tested in monkeys

4. microRNA statistics Many are highly conserved MIRHG2 microRNA host gene 2 (non-protein coding) DLEU2 deleted in lymphocytic leukemia 2 (non-protein coding) HOXD4 homeobox D4 Probably >1000 miRNAs in mammalian genomes Identified presently (March 2009) - 706 human miRNAs - 547 mouse miRNAs - 286 rat miRNAs May modulate the expression of at least 30% of all protein coding genes in a genome ~60% of miRNAs are expressed independently ~15% are encoded in clusters ~25% are found in introns

5. microRNA synthesis

6. MicroRNA-mRNA interaction 3´ 5´ 3´

7. microRNA function

9. microRNAs targeting 3’UTRs Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals (Xie et al., 2005)

10. microRNAs targeting CDS A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence (Forman et al., 2008)

11. microRNA target prediction

12. Seed conservation

13. microRNAs target specific processes

14. microRNA regulatory principles

15. microRNA silencing

16. microRNA overexpression pri-miRNA

17. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq)