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MicroRNAs, miRBase and deep sequencing Sam Griffiths-Jones - - PowerPoint PPT Presentation
MicroRNAs, miRBase and deep sequencing Sam Griffiths-Jones - - PowerPoint PPT Presentation
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
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He and Hannon (2004)
- Nat. Reviews. Genet.
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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
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Intronic miRNAs
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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
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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
- f 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
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He and Hannon (2004)
- Nat. Reviews. Genet.
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Deep sequencing data
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So what?
- Show isomiRs
- Read counts are proxy for expression
- Search by experiment, tissue, stage
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Expression analysis
embryo brain testes
- vary
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So what?
- Show isomiRs
- Read counts are proxy for expression
- Search by experiment, tissue, stage
- Evaluate dubious annotations
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He and Hannon (2004)
- Nat. Reviews. Genet.
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Deep sequencing data
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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.
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High confidence miRNAs
Proportion of miRNAs included in high confidence set
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Challenges
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Community annotation
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