A turbo intro to (the bioinformatics of) microRNAs
11/6 2009Peter Hagedorn
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).
microRNA research
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microRNAs discoveredin human, mice, and Drosophila
microRNAs implicatedin leukemia
microRNAs identifiedin viral genomes
Drugs againstmicroRNAs testedin monkeys
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 genomesIdentified 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
microRNA synthesis
MicroRNA-mRNA interaction
3´ 5´
5´ 3´
microRNA function
microRNA function
microRNAs targeting 3’UTRs
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals (Xie et al., 2005)
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)
microRNA target prediction
Seed conservation
microRNAs target specific processes
microRNA regulatory principles
microRNA silencing
microRNA overexpression
pri-miRNA
Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq)