Download MiRNA_GO_Meeting_August2015

microRNA GO annotation
www.ucl.ac.uk/functional-gene-annotation
Why annotate miRNAs?
Direct curation of the roles of miRNAs is expected to improve
miRNA functional analysis that has so far relied on indirect
analysis of the gene targets’ functions
“We show that the most commonly used functional
enrichment test is inappropriate for the analysis of
sets of genes targeted by miRNAs.” Bleazard et al. 2015
Scope of annotation guidelines
miRNAs can affect gene regulation in many ways
The focus of our guidelines is on gene silencing by miRNA
via the 3’UTR of mRNAs, including;
• annotation of the protein components of the canonical mammalian
miRNA processing pathway
• annotation of proteins that affect the levels of miRNAs
• annotation of the miRNA’s role in gene silencing
• annotation of the miRNA targets
• contextual annotation of miRNA regulation
Guideline examples
• annotation of the protein components of the canonical
mammalian miRNA processing pathway
Annotation of proteins involved in miR processing
Animals
GO terms
to apply
All human proteins
involved in miR
processing have
been annotated
with these roles
Over 250
annotations
miR processing proteins
Plants
miPEPs – newly discovered
peptide regulators of miRNA
transcription encoded by
miRNA genes
Guideline examples
• annotation of the miRNA’s role in gene silencing
New biology = ontology developments
New GO terms added for miRNA processing
deadenylation involved in gene silencing by miRNA
GO:0098806
mRNA cleavage involved in gene silencing
GO:0098795
endoribonuclease activity, cleaving miRNA-paired mRNA
GO:0090624
pre-mRNA transporter activity
GO:0090631
regulation of production of miRNAs involved in gene silencing by miRNA
GO:1903798
- negative regulation of production of miRNAs involved in gene silencing by miRNA
GO:1903799
- positive regulation of production of miRNAs involved in gene silencing by miRNA
GO:1903800
miRNA role in gene silencing
• Translational repression
• mRNA deadenylation
• mRNA cleavage
Ontology updates – May 2015
Gene silencing
mRNA
deadenylation
mRNA
cleavage
Translation
regulation
All silencing roles of miRNAs
now come under gene silencing
by miRNA
www.ebi.ac.uk/QuickGO
GO terms for miRNA roles
Translational repression
GO:0035195
gene silencing
by miRNA
GO:0035278
negative regulation
of translation
involved in gene
silencing by miRNA
GO:1903231
mRNA binding
involved in
posttranscriptional
gene silencing
GO:0035279
GO:0098806
mRNA deadenylation
deadenylation
involved in
gene silencing
by miRNA
mRNA cleavage
involved in gene
silencing by
miRNA
mRNA cleavage
Evidence codes
1. Increasing levels of miRNAs
e.g. pri-miRNA, pre-miRNA, miRNA mimic
Evidence code = Inferred from Direct Assay (IDA)
2. Decreasing levels of miRNAs
e.g. antagomir, antisense-miRNA, blockmir, miRNA
eraser or sponge, miRNA knockout
Evidence code = Inferred from Mutant Phenotype (IMP)
Guideline examples
• annotation of the miRNA targets
miRNA targets
• Predicted
Sequence alignment of
miRNA with mRNA
• Validated binding
miRNA shown to act directly on a
mRNA by e.g. reporter assay or
Co-IP plus change in mRNA levels
• Validated other
no evidence of direct action, but
levels of mRNA are affected in
response to miRNA, e.g. Western, qPCR
Guidelines for miRNA target annotation
Guideline examples
• contextual annotation of miRNA regulation
Capturing cell types
Important for
pathway
analysis
miR-195 and miR-29b regulate extracellular matrix expression in smooth muscle cells (SMCs).
Elastin expression in SMCs following overexpression of miR-195 or miR-29b as assessed by qPCR.
(PMID:25201911)
Capturing physiological effects of silencing
Important for
functional
analysis of
miRNAs
microRNA-133 (miR-133) modulates cAMP signaling in vitro. A, Effect of miR-133 on adenylyl cyclase (AC)
activity in cardiomyocytes. Bars indicate SEM. (PMID:24807785)
Summary
When annotating a miRNA we should minimally aim to capture the following:
1. The miRNA’s main role in gene silencing and its target(s);
gene silencing by miRNA
negative regulation of gene expression
mRNA binding involved in post-transcriptional gene silencing by miRNA
target mRNA indicated in the annotation extension
2. The effect of silencing the target mRNA;
e.g. if an adenylate cyclase transcript was silenced:
negative regulation of adenylate cyclase activity
negative regulation of cAMP biosynthetic process
3. The relevance of that process it regulates;
e.g. negative regulation of adenylate cyclase activity involved in heart contraction
Practical use of Guidelines
The BHF-UCL cardiovascular miRNA annotation project
The aims of the microRNA GO annotation project are to:
✔
draw up guidelines for consistent literature-based annotation of miRNAs in
consultation with the GO Consortium and miRNA experts
•
functionally annotate miRNAs that are involved with cardiovascular
development and related processes
•
capture the targets of the cardiovascular-related miRNAs
77
174
121
372 annotations
Thank You
miRNA experts
Curators
Lars Maegdefessel
Manuel Mayr
Anna Zampetaki
Anastasia Kalea
Dmitry Sitnikov
Leonore Reiser
Reactome curators
From: MicroRNA gets down to business
George S Mack
Nature Biotechnology 25, 631 - 638 (2007)