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)