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MicroRNAs, miRBase and deep sequencing Sam Griffiths-Jones - PowerPoint PPT Presentation

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MicroRNAs, miRBase and deep sequencing Sam Griffiths-Jones Trainer: Sam Griffiths-Jones He and Hannon (2004) Nat. Reviews. Genet. How many miRNAs? Human Fly Mature miRNAs 2588 466 w/ validated targets 587 (23%) 39 (8%) Pre-miRNAs

  1. MicroRNAs, miRBase and deep sequencing Sam Griffiths-Jones

  2. Trainer: Sam Griffiths-Jones

  3. He and Hannon (2004) Nat. Reviews. Genet.

  4. How many miRNAs? Human Fly Mature miRNAs 2588 466 w/ validated targets 587 (23%) 39 (8%) Pre-miRNAs 1881 256 In introns 841 (44%) 111 (43%) Clustered (<10 kb) 468 (35%) 88 (34%) miRBase v21 miRTarBase v4.5

  5. Intronic miRNAs

  6. Clustered microRNAs Lee Y et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004 23:4051:4060 Ryazansky SS, Gvozdev VA, Berezikov E. Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila . BMC Genomics . 2011 12:371

  7. miRBase aims to curate a consistent nomenclature scheme by which novel • microRNAs are named to act as the central repository for all published microRNA • sequences, and to facilitate online searching and bulk download of all microRNA data to provide human-readable and computer-parsable annotation of • microRNA sequences (for example, functional data, references, genome mappings) to provide access to the primary evidence that supports • microRNA annotations to link to and aggregate microRNA target predictions and • validations

  8. He and Hannon (2004) Nat. Reviews. Genet.

  13. Deep sequencing data

  14. So what? • Show isomiRs • Read counts are proxy for expression • Search by experiment, tissue, stage

  15. Expression analysis ovary testes brain embryo

  16. So what? • Show isomiRs • Read counts are proxy for expression • Search by experiment, tissue, stage • Evaluate dubious annotations

  17. He and Hannon (2004) Nat. Reviews. Genet.

  18. Deep sequencing data

  19. High confidence miRNAs • Both arms >10 reads • 2 nt 3’ overhang (+/- 2) • >50% of reads have same 5’ end • Hairpin FFE < -0.2 kcal/mol/nt. • >60% of mature nts paired Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014 42:D68-D73.

  20. High confidence miRNAs Proportion of miRNAs included in high confidence set

  24. Challenges

  25. Community annotation

  26. http://www.mirbase.org/tutorials/ ebi-2015-06-17/

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