MiRNA Questionnaire
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working group discussion March14
pdf of presentation File:GOCmiRNA2014.pdf
Questionnaire based on Inhibition of microRNA-29b reduces murine abdominal aortic aneurysm (AAA) development, PMID: 22269326
Links survey monkey questions
short version of miRNA annotations
Question 1
Figure 1: Murine model of experimental abdominal aortic aneurysm: the porcine pancreatic elastase (PPE) infusion model in C57BL/6 mice
Possible annotation porcine elastase with GO:0030198 extracellular matrix organization IDA
Agreed that no-one would annotate this due to very artificial system
Question 2
Cells were treated with human TGF-β1
- Known regulator of miR-29b
- Profibrotic stimulus
- Treatment decreased miR-29b expression in hAFBs but not in hASMCs
Suggested annotation: Human TGF-β1 GO:2000628 regulation of miRNA metabolic process IDA C16: has_regulation_target human miR-29b, occurs_in CL:0002547 fibroblast of the aortic adventitia
Would you include the cell specific information in the annotation extension field associated with your annotation of TGF-β1?
Question 3
Should there be a GO term specific for the miRNAs?
Eg ‘miRNA activity involved in gene silencing’ Parent terms: has_part GO:0003729 mRNA binding part_of GO:0035195 gene silencing by miRNA is_a molecular_function. Definition: Interacting selectively and non-covalently with an RNA sequence in order to modulate translation.
Note that proteins are annotated to the term GO:0035195 gene silencing by miRNA
Question 4
To apply the GO term 'GO:0035195 gene silencing by miRNA' to a miRNA would there have to be evidence in this paper that this miRNA bound to the target mRNA?
Question 5
Figure 3B Primary aortic fibroblasts were treated with human TGF-β1 Known regulator of miR-29b Profibrotic stimulus
Expression levels of miR-29b target genes (COL1A1, COL3A1, ELN, FBN1) in Tgf-β–stimulated anti-29b– and pre-29b–transfected hAFBs were measured.
Results COL1A1 and COL3A1 were significantly up-regulated with Tgf-β-stimulation COL1A1 and COL3A1 further up-regulated with anti-29b treatment COL1A1 and COL3A1 down-regulated with pre-29b
If the anti-29b data was not available the experimental data involving the addition of pre-29b could be annotated as IDA (or IMP) as:
Annotation: Human miR-29b: GO:0035195 gene silencing by miRNA IDA C16: has_ regulation_target human COL1A1 [and COL3A1] happens_during GO:0071560 cellular response to transforming growth factor beta stimulus.
As this experiment involves the addition of an miR which is known to be expressed in these cells would you also include the C16 statement: occurs_in CL:0002547 fibroblast of the aortic adventitia?
Question 6
Following on from the previous question: Figure 3B assuming the addition of pre-29b was annotated as: Human miR-29b: GO:0035195 gene silencing by miRNA IDA C16: has_ regulation_target human COL1A1 [and COL3A1] happens_during GO:0071560 cellular response to transforming growth factor beta stimulus.
If the miR was not known to be expressed in fibroblast of the aortic adventitia cells would you also include the C16 statement: occurs_in CL:0002547 fibroblast of the aortic adventitia?
Question 7
Figure 5D-F demonstrates a change in MMP activity MMPs are matrix metalloprotease associated with ECM degradation
Results (F) Mmp2 and Mmp9 expression up-regulated with pre-29b Mmp2 and Mmp9 expression down-regulated with anti-29b Note that this is not gene silencing of MMPs, but the reverse! Ie there is likely to be other genes being regulated before these.
Annotation suggestion: Mouse miR-29b GO:0090091 positive regulation of extracellular matrix disassembly IMP
Do you think this interpretation is too downstream from the observed increase in MMP activity?
Question 8
The custom-made LNA-anti-miR-29b 5′-3′ sequence aligns 100% with two human sequences (in 2 genomic sites)
Would you expect both miRs to be annotated based on the anti-29b experiments?
Supported with the IGI evidence code and the WITH field including the other miR sequence
Question 9
When associating 'GO:0035195 gene silencing by miRNA' with a miRNA, based on an experiment using an anti-miR to demonstrate up-regulation of specific mRNA levels in the absence of the miR,
How do we decide whether or not an mRNA is a direct target of a miRNA?