miRNA annotation guidelines

[gocentral]

Please write your comments about the miRNA annotation guidelines in this issue.

Reported by: rachhuntley

Original Ticket: geneontology/annotation-issues/1292

[gocentral]

on behalf of TAIR.

Something new to consider that may be relevant for more than plants.

ISSUE A. The case of peptide encoding miRNA’s (once again, plants lead …)
The existence of small functional ORFs encoded by pri-miRNA’s in plants was recently reported by Lauressergues, et.al. (doi:10.1038/nature14346 ). Essentially they have demonstrated that there are ORFs in pri-miRNA’s that encode small peptides. The paper describes a new class of gene products they are calling miPEPs (micro RNA encoded peptide). They show that pri-miR171b of Medicago truncatula and the pri-miR165a of Arabidopsis encode functional peptides that influence the accumulation of their respective miRNAs. Overexpression of each peptide results in an increase of their respective pri-miRNAs. They show that the overexpression phenotype is suppressed in RNA Pol II background suggesting that the action of the miPEP is via transcriptional regulation. It is likely that this how/why pri-miRNA’s have been shown increase their own expression.

With respect to the guidelines p.9 discusses annotations to components that increase the levels of miRNA which is what at least some of these buggers are doing.

1. With respect to new annotations that come out of this we can probably annotate the miPEP to GO:0010628 positive regulation of gene expression with annotation extension to: regulates_levels_of_product_of: miRNA or pri-miRNA and GO:1902895, positive regulation of pri-miRNA transcription from RNA polymerase II promoter
2. To be consistent with the guidelines the evidence for the first is IMP for at least the experiments where the evidence is from overexpression of the miPEP protein product. For the second, it may depend on how it is done going forward. For this paper it is IGI. The overexpression construct was crossed with RNA pol II mutant and that abolished the activity of the overexpressed miPEP.

ISSUE B. This also raises some issues in terms of annotating the miRNA locus that may be specific to each database that we should discuss and plan for.

How will the annotation be done- to the level of the locus or gene product? Probably to the level of product since this is a function associated to the protein product not the miRNA or pri-miRNA product. Each DB would need to figure out how to represent and annotate the miPEPs (assuming this is a phenomenon that is more broadly represented in species besides plants).

ISSUE C. Clarification. A general comment on the guidelines. We found the tables hard to read/get through and thought that a flow chart or decision tree in some cases would more effectively communicate the process of annotating.

Original comment by: reiserl

[gocentral]

Also from TAIR: Table 2 is very difficult to use, we suggest using a decision tree approach instead.

Original comment by: tberardini

[gocentral]

Hi Leonore,

Firstly, thank you very much for reading the document and providing feedback.

This recent development is pretty interesting and I agree that it’s something that we should add to the guidance, but I’m wondering that because it has only been demonstrated in plants so far, whether it is something to add to a plant-specific section? To determine this, I’d need an answer to my second question from my initial email "do you think you would need any modifications to the guidelines for the annotation of miRNAs in your species? If so would you be willing to write a stand-alone section which describes how you would differently annotate miRNAs or the biogenesis pathway for your particular species of interest? This will enable curators to easily pinpoint the section of the guidelines they need to read for a particular species.”

As the guidelines stand now, do they fit with how you would annotate plant miRNAs? If so, then we could easily add in a paragraph about the miPEPs that can be extended if/when these are found in other species.

As for the section it refers to, the "increasing miRNA levels" section is more about the experimental techniques that are used by authors to modulate miRNAs, the example you have sent is a mechanism by which the pri-miRNAs are regulated in the plant, so I would see it fitting better into the section "Annotating an entity regulating levels of an mRNA, when mediated by miRNA”.

I largely agree with your suggestions for annotations. i.e. could annotate the miPEP with: GO:0010628 positive regulation of gene expression with annotation extension to: regulates_levels_of_product_of: pri-miRNA

Or, if they show regulation of transcription GO:1902895, positive regulation of pri-miRNA transcription from RNA polymerase II promoter with annotation extension to: regulates_levels_of_product_of: pri-miRNA

Depending on the evidence given you may want to capture both of these annotation with different evidence codes (some groups capture the different evidence, but I think our group would only capture the most specific GO term, i.e. the second one), but we needn’t specify an evidence code in the documentation as it would depend on the individual experiment.

Also, if they show an effect on levels of mature miRNAs, you could additionally use: GO:1903800 positive regulation of production of miRNAs involved in gene silencing by miRNA with annotation extension to: regulates_levels_of_product_of: miRNA

As for the second issue, I definitely agree that we should, where possible, capture this on the level of the product. I don’t know if these sequences are something that would end up in UniProt, I can ask them.

Thanks again, Rachael.

Original comment by: rachhuntley

[gocentral]

Hi Tanya,

I will take a look at converting the table into a decision tree.

Thanks for your feedback! Rachael.

Original comment by: rachhuntley

[gocentral]

Hi Rachael,

Thanks for putting together the guidelines for miRNA curation.

One question I had was actually about the ontology and the placement of miRNA-associated terms under the parent GO:0016458, gene silencing.

The current definition of this term is: Any transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.

I don't know if all instances of gene silencing by miRNA can be considered 'long-term'.

If not, then perhaps the definition of 'gene silencing' or the placement of its child miRNA terms in the ontology might need revision?

We have a few direct annotations to the term that I'd like to review to see if we can make more specific annotations.

Thanks, --Kimberly

Original comment by: vanaukenk

[gocentral]

Hi Kimberly,

That's a good point, I hadn't looked closely at the parent. The gene silencing we are talking about is not long-term, that seems to cover more the imprinting and inherited type of gene silencing.

I will open a SourceForge issue for the editors to take a look, hopefully they can just broaden the definition.

Thanks, Rachael.

Original comment by: rachhuntley

[gocentral]

Original comment by: rachhuntley

[gocentral]

I have made a decision tree to replace Table 2 in the guidelines (attached at the top). Feel free to add any comments you have to this ticket.

Original comment by: rachhuntley

[gocentral]

Rachael Certainly decisions regarding miPEPs can be delayed until we learn how pervasive they are. Internally we are going to have to figure out how to include those gene products as well so be good to know where UniProt will stand on that issue.

There are some differences in the plant v animal biogenesis pathways. For example, all of the pri-premiRNA processing steps occur in the nucleus (mediated by DCL1) whereas in metazoans it is segregated in the nucleus and then cytoplasm. But that should not affect annotations. Plant miRNA's are also methylated.

I don't know about a stand alone section but I can try generating an annotated illustration similar to your figure 1- or just the table highlighting a few of the differences. Because of how we do our annotations we haven't systematically annotated (or re annotated) all of the components of the miRNA biogenesis pathway- which makes it a little more time consuming.

And then of course there is that dodgy issue of some of the key papers in this field being retracted due to fraud... gotta love empiricism.

Original comment by: reiserl

[gocentral]

Update on miPEP sequences: UniProt have now included the miPEP sequences from Lauressergues, et.al. (doi:10.1038/nature14346), which I have sent to TAIR.

Original comment by: rachhuntley

[gocentral]

rachael, here is my attempt at a version of your figure 1 trying to summarize salient entities and differences in miRNA biogenesis in plants.

Original comment by: reiserl

[gocentral]

Hi Leonore, Just to say thanks for this, I am going through this now so I'll send you some comments shortly! Rachael.

Original comment by: rachhuntley

[gocentral]

Here is some feedback from Dmitry from MGI. My responses are prefixed with a 'RH>'.

Hi Rachael,

Below are my notes and suggestions.

1/ Fig 1. Change DCRG8 to DGCR8

RH>OK, thanks for spotting this

2/ I do not know how extensive the list of annotation examples on Fig 1 should be. Below I collected some miRNA related annotations for AGO1-4, which you might find useful. Some of them are not on Fig 1.

RH>I’ve added comments below for each one

3/ Page 6. You mention here: "...consider the intentions and interpretations of the author." I think that this is an important point, which could be repeated in other sections or expanded a little bit here. For example, when a curator is unsure about the annotation, he/she can see what conclusions the authors make.

RH>OK, I will draft something, but I think it is also important to be cautious with what the author is saying, for example if they say that mRNA X is a target of miRNA Y with no corroborating evidence, I wouldn’t be happy – I would want to see a sequence alignment or some evidence in the miRNA target prediction databases as well. For the miRNAs involvement in regulating a biological process on the other hand, I’d be happy to go with the authors intentions in addition to the evidence they presented in the paper.

4/ On page 20 Should this "Mutation of either the Let-7i binding site in IL2 or..." be "Mutation of either the Let-7i binding site in IL2 promoter or..."

RH>Yes, you’re right, I’ve changed this.

5/ On page 21 Should this GO:0001046 (core promoter sequence-specific DNA binding) be GO:0000979 (RNA polymerase II core promoter sequence-specific DNA binding)

RH>Again, you’re right. I’ve changed this as well.

6/ I think the summary section could be a little expanded. Maybe shortly mentioning again the flow of the curation process. And summarizing what the usual problems are for miRNA curators.

RH>Could you help me out here and suggest what problems you have encountered? Personally, I have trouble sometimes finding the correct identifier for a miRNA, especially if they don’t present a sequence, and also finding evidence that an mRNA is a predicted target of a miRNA.

Dmitry's response - I also agree with the two main problems you mention. You could also address when the paper discusses for example mir1000 but there are mir1000a, mir1000b, mir1000c etc.

Overall, I liked the draft and found it to be very helpful and useful for myself. One question I would like to ask, just to clarify it for myself. This relates to Experimental Techniques on page 15. PCR measures the transcription step in the gene expression pathway. So when PCR is used, instead of "regulation of transcription" terms I should use "regulation of gene expression" terms, is that correct?

RH>I have not seen any experiments that use straight PCR, it is usually quantitative RT-PCR so they are measuring the levels of mRNA present. PCR is just amplification of DNA, it’s not quantitative either, unless it’s qPCR – I don’t regard it as a measure of transcription. I guess I don’t really understand what you are saying.

Thanks, Dmitry.

---

AGO1

GO:0000932 cytoplasmic mRNA processing body IDA

RH>This paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893129/ shows that only approx. 1% of AGO is present in P-bodies, the rest being distributed in the cytoplasm. The paper also mentions that P-bodies are not required for miRNA-induced silencing. Based on this, I wouldn’t put P-body as a recommended GO annotation, but I can include a note that if the experiment shows localization of a protein/miRNA in a P-body, then you can annotate to ‘cytoplasmic mRNA processing body’. What do you think?

GO:0035068 micro-ribonucleoprotein complex IDA

RH>I have just opened a SourceForge ticket to ask whether this term should be a child of 'RISC complex’ as it looks like it should. The ticket is here https://sourceforge.net/p/geneontology/ontology-requests/11664/

GO:0010586 miRNA metabolic process IDA

RH>AGO proteins only bind to miRNAs, they don’t appear to be involved in their metabolism – It looks like you have pulled this from an actual annotation, so I’ll be sure to go and review this.

AGO2

GO:0070578 RISC-loading complex IDA

RH>This is included under the ‘RISC-loading complex proteins’ section, in brackets it says AGO1-4. I will try to make this clearer.

GO:0035068 micro-ribonucleoprotein complex IDA

RH>As above

GO:0000932 cytoplasmic mRNA processing body IDA

RH>As above

(GO:0035198 miRNA binding IDA , IMP )

RH>This annotation is under the 'Argonautes (AGO1-4)' section

GO:0004521 endoribonuclease activity IDA

RH>I have suggested the more specific term GO:0090624 endoribonuclease activity, cleaving miRNA-paired mRNA in the ‘AGO2’ section

GO:0035279 mRNA cleavage involved in gene silencing by miRNA IDA

RH>This is suggested in the ‘AGO2’ section

GO:0010586 miRNA metabolic process IDA

RH>As above

GO:0035280 miRNA loading onto RISC involved in gene silencing by miRNA ISO Human

RH>This is included under the ‘RISC-loading complex proteins’ section, in brackets it says AGO1-4. I will try to make this clearer.

GO:0006379 mRNA cleavage IMP

RH>The more specific term GO:0035279 mRNA cleavage involved in gene silencing by miRNA is suggested in the ‘AGO2’ section

GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic IDA

RH>The child term of this GO:0090624 endoribonuclease activity, cleaving miRNA-paired mRNA is suggested in the ‘AGO2’ section

GO:0035278 negative regulation of translation involved in gene silencing by miRNA ISO Human

RH>This annotation is under the 'Argonautes (AGO1-4)' section

AGO3

GO:0035068 micro-ribonucleoprotein complex IDA

RH>As above

AGO4

GO:0035068 micro-ribonucleoprotein complex IDA

RH>As above

GO:0000932 cytoplasmic mRNA processing body IDA

RH>As above

Original comment by: rachhuntley

[gocentral]

Hi Leonore,

Thanks very much for putting together the annotations for the plant pathway. My first thought is that to avoid any problems with replicating published figures, I have made my own figure for the animal pathway and I think it would look nice if we have the same style figure for the plant pathway. Would you be able to do this using my Powerpoint file (Figure 1 attached here) as a basis, i.e. just move the blobs around and re-name them? If you don't have time, I can do this.

Also, if we could keep the same style with the suggested GO terms on the left, that would be great. I think the table below could be condensed somewhat by grouping the GO terms that are the same for each complex, e.g. you could have the heading “Nuclear dicing complex” (DCL1, SE, HYL, DDL, TGH) and put all the GO terms that are common to these proteins under that heading, similar to how I did the RISC-loading complex. Any proteins that have separate annotations, e.g. DCL1, could come after that section. I also have some comments about the GO terms you used, which I have added as comments in blue to the attached file.

Thanks again, Rachael.

Original comment by: rachhuntley

[gocentral]

Figure 1 Powerpoint file here

Original comment by: rachhuntley

[gocentral]

This is a really nice figure Rachael, Leonore thanks for suggesting this. I'm sure curators are going to find this very useful. Ruth

Original comment by: RLovering

[gocentral]

Rachael I saw your comments and will edit accordingly. I can try and update the figure in the next days as well.

Ruth? You are welcome but not sure what you are referring to?

Leonore Reiser, Ph.D.

lreiser@arabidopsis.org 510-761-6091

On Thu, Apr 30, 2015 at 6:54 AM, Ruth lovering@users.sf.net wrote:

This is a really nice figure Rachael, Leonore thanks for suggesting this. I'm sure curators are going to find this very useful.

Ruth

• [annotation-issues:#1292] http://sourceforge.net/p/geneontology/annotation-issues/1292 miRNA annotation guidelines*

Status: open Group: UCL Labels: miRNA Created: Fri Mar 20, 2015 11:46 AM UTC by rach_huntley Last Updated: Thu Apr 30, 2015 09:08 AM UTC Owner: rach_huntley

Please write your comments about the miRNA annotation guidelines in this

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Original comment by: reiserl

[gocentral]

Hi Leonore,

Have you had chance to work on the plant miRNA section and figure? I have had some feedback from various people and am getting close to having a final version of the guidelines, so it would be great to include the plant section before I put a version on the wiki.

Thanks for your help. Rachael.

Original comment by: rachhuntley

[gocentral]

Rachel Sorry been working on a manuscript go waylaid by some emergencies, and this got pushed down in the queue. I can probably send the editorial changes later today or tomorrow but realistically don't know that I can make you a new figure in the time frame you need.

Leonore

Leonore Reiser, Ph.D.

lreiser@arabidopsis.org 510-761-6091

On Wed, Jun 10, 2015 at 6:15 AM, rach_huntley huntley@users.sf.net wrote:

Hi Leonore,

Have you had chance to work on the plant miRNA section and figure? I have had some feedback from various people and am getting close to having a final version of the guidelines, so it would be great to include the plant section before I put a version on the wiki.

Thanks for your help.

Rachael.

• [annotation-issues:#1292] http://sourceforge.net/p/geneontology/annotation-issues/1292 miRNA annotation guidelines*

Status: open Group: UCL Labels: miRNA Created: Fri Mar 20, 2015 11:46 AM UTC by rach_huntley Last Updated: Thu Apr 30, 2015 01:54 PM UTC Owner: rach_huntley

Please write your comments about the miRNA annotation guidelines in this

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Original comment by: reiserl

[gocentral]

Hi Kimberly,

Just to let you know this was dealt with in this SF ticket https://sourceforge.net/p/geneontology/ontology-requests/11638/ David has broadened the definition of gene silencing.

Rachael.

Original comment by: rachhuntley

[gocentral]

Hi Leonore, OK, thanks. If you can send me what you can, I will try to work on the figure. We could add the plant section later though if it's going to take a while longer.

Rachael.

Original comment by: rachhuntley

[gocentral]

Rachel I made some of the changes with the table and probably created a few more questions. I agree about the need to add some terms. Take a look at this table and then maybe we can resolve the few questions that came up as I was organizing the new table.

Leonore Reiser, Ph.D.

lreiser@arabidopsis.org 510-761-6091

On Thu, Jun 11, 2015 at 2:00 AM, rach_huntley huntley@users.sf.net wrote:

Hi Leonore, OK, thanks. If you can send me what you can, I will try to work on the figure. We could add the plant section later though if it's going to take a while longer.

Rachael.

• [annotation-issues:#1292] http://sourceforge.net/p/geneontology/annotation-issues/1292 miRNA annotation guidelines*

Status: open Group: UCL Labels: miRNA Created: Fri Mar 20, 2015 11:46 AM UTC by rach_huntley Last Updated: Wed Jun 10, 2015 01:15 PM UTC Owner: rach_huntley

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Original comment by: reiserl

[gocentral]

Hi Leonore,

I have made a diagram for the plant miRNA biogenesis pathway (attached and legend below), if you wouldn't mind having a look?

I also had some comments on the table of annotations you sent, which may explain some of my choices of GO terms in the figure (also attached).

I have made a draft of the plant section for the guidelines, if you would like to comment on that as well, that would be great (see text below).

Thanks very much. Rachael.

Legend for Figure 2. The canonical plant miRNA processing pathway. The proteins involved in the pathway of miRNA formation are shown together with the annotations that they are expected to be associated with. Abbreviations: Not2b: Negative on TATA-less 2B; CDC5: Cell division cycle 5; Mediator complex proteins include: MEDIATOR21 (AT4G04780), MEDIATOR14 (AT3G04740), MEDIATOR25 (AT1G25540), MEDIATOR20a (At2g28230), MEDIATOR20b (At4g09070), MEDIATOR20c (At2g28020); miPEP: miRNA encoded peptide; DCL1: Dicer-like 1; SE: Serrate; HYL1: Hyponastic leaves 1; DDL: Dawdle; TGH: Tough; CBP20: Cap binding complex protein 20; CBP80: Cap binding complex protein 80; HEN1: Hua enhancer 1; HST: Hasty; HSP90: Heat shock protein 90; SQN: Squint; AGO: Argonaute.

Plant miRNA biogenesis. The canonical plant miRNA biogenesis pathway (Figure 2) shares some commonalities with the mammalian pathway, however there are some major differences. In plants miRNA biogenesis is largely completed within the nucleus. All of the processing steps involving the pri- and pre-miRNAs and carried out by DCL1 occur in the nucleus, whereas in mammals these processes are separated between the nucleus and cytoplasm (see Figure 1). In addition, the plant miRNA duplex is stabilized after cleavage by 2’-O-methylation by the Hua enhancer 1 protein. In a recent paper, Lauressergues et al. describe microRNA regulatory peptides (miPEPs) that are produced from primary miRNA transcripts. These peptides activate the transcription of the primary miRNAs they derive from, resulting in accumulation of the corresponding mature miRNAs. It is too early to say whether miPEPs are conserved in mammals.

There are also differences in target recognition between mammalian and plant miRNAs. Plant miRNAs require perfect, or near-perfect complementarity with the target mRNA, whereas mammalian miRNAs generally only have complementarity with their targets within the seed region. The target mRNAs are silenced most commonly by cleavage, although there are many mRNAs that instead undergo translational repression. Currently, there is no evidence that miRNAs are involved in mRNA destabilization by deadenylation.

References: Rogers, K and Chen, X., (2013) The Plant Cell 25: 2383-2399 (http://dx.doi.org/10.1105/tpc.113.113159) Xie, e.al., (2015) , Cell. Mol. Life Sci. 72:87–99 (DOI 10.1007/s00018-014-1728-7 ) Lauressergues (2015) Nature 520, 90–93 (doi:10.1038/nature14254) Axtell MJ et al.,( 2011), Genome Biology 12:221 (doi:10.1186/gb-2011-12-4-221)

Original comment by: rachhuntley

[gocentral]

Hi Rachael, The figure looks nice. Thanks for doing that. Definitely not comprehensive as your note indicates. This is something of a reflection of how we do curation, on a per gene/paper basis rather than tackling a whole pathway at once. Hard choices we get to make with limited staff, you know.

Anyway I made some comments on the document you sent. See if it makes sense.

Leonore Reiser, Ph.D.

lreiser@arabidopsis.org 510-761-6091

On Mon, Jun 29, 2015 at 7:05 AM, rach_huntley huntley@users.sf.net wrote:

Hi Leonore,

I have made a diagram for the plant miRNA biogenesis pathway (attached and legend below), if you wouldn't mind having a look?

I also had some comments on the table of annotations you sent, which may explain some of my choices of GO terms in the figure (also attached).

I have made a draft of the plant section for the guidelines, if you would like to comment on that as well, that would be great (see text below).

Thanks very much. Rachael.

Legend for Figure 2. The canonical plant miRNA processing pathway. The proteins involved in the pathway of miRNA formation are shown together with the annotations that they are expected to be associated with. Abbreviations: Not2b: Negative on TATA-less 2B; CDC5: Cell division cycle 5; Mediator complex proteins include: MEDIATOR21 (AT4G04780), MEDIATOR14 (AT3G04740), MEDIATOR25 (AT1G25540), MEDIATOR20a (At2g28230), MEDIATOR20b (At4g09070), MEDIATOR20c (At2g28020); miPEP: miRNA encoded peptide; DCL1: Dicer-like 1; SE: Serrate; HYL1: Hyponastic leaves 1; DDL: Dawdle; TGH: Tough; CBP20: Cap binding complex protein 20; CBP80: Cap binding complex protein 80; HEN1: Hua enhancer 1; HST: Hasty; HSP90: Heat shock protein 90; SQN: Squint; AGO: Argonaute.

Plant miRNA biogenesis. The canonical plant miRNA biogenesis pathway (Figure 2) shares some commonalities with the mammalian pathway, however there are some major differences. In plants miRNA biogenesis is largely completed within the nucleus. All of the processing steps involving the pri- and pre-miRNAs and carried out by DCL1 occur in the nucleus, whereas in mammals these processes are separated between the nucleus and cytoplasm (see Figure 1). In addition, the plant miRNA duplex is stabilized after cleavage by 2’-O-methylation by the Hua enhancer 1 protein. In a recent paper, Lauressergues et al. describe microRNA regulatory peptides (miPEPs) that are produced from primary miRNA transcripts. These peptides activate the transcription of the primary miRNAs they derive from, resulting in accumulation of the corresponding mature miRNAs. It is too early to say whether miPEPs are conserved in mammals.

There are also differences in target recognition between mammalian and plant miRNAs. Plant miRNAs require perfect, or near-perfect complementarity with the target mRNA, whereas mammalian miRNAs generally only have complementarity with their targets within the seed region. The target mRNAs are silenced most commonly by cleavage, although there are many mRNAs that instead undergo translational repression. Currently, there is no evidence that miRNAs are involved in mRNA destabilization by deadenylation.

References: Rogers, K and Chen, X., (2013) The Plant Cell 25: 2383-2399 ( http://dx.doi.org/10.1105/tpc.113.113159) Xie, e.al., (2015) , Cell. Mol. Life Sci. 72:87–99 (DOI 10.1007/s00018-014-1728-7 ) Lauressergues (2015) Nature 520, 90–93 (doi:10.1038/nature14254) Axtell MJ et al.,( 2011), Genome Biology 12:221 (doi:10.1186/gb-2011-12-4-221)

Attachment: Plant_miR_Biogenesis_Figure.png (505.5 kB; image/png) Plant_miRNA_Table_v2_Leonore_RH.docx (143.6 kB;

application/vnd.openxmlformats-officedocument.wordprocessingml.document)

• [annotation-issues:#1292] http://sourceforge.net/p/geneontology/annotation-issues/1292 miRNA annotation guidelines*

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Original comment by: reiserl

[gocentral]

Hi Leonore,

Was there an attachment? I can't seem to see it.

Thanks, Rachael.

Original comment by: rachhuntley

[gocentral]

hopefully now attached.

Leonore Reiser, Ph.D.

lreiser@arabidopsis.org 510-761-6091

On Tue, Jun 30, 2015 at 3:03 AM, rach_huntley huntley@users.sf.net wrote:

Hi Leonore,

Was there an attachment? I can't seem to see it.

Thanks,

Rachael.

• [annotation-issues:#1292] http://sourceforge.net/p/geneontology/annotation-issues/1292 miRNA annotation guidelines*

Status: open Group: UCL Labels: miRNA Created: Fri Mar 20, 2015 11:46 AM UTC by rach_huntley Last Updated: Mon Jun 29, 2015 02:05 PM UTC Owner: rach_huntley

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Original comment by: reiserl

[gocentral]

Hi Leonore,

Thanks for the document, it all makes sense.

For the transcription factors, I think we would annotate them as we would any other TF, the only difference being that we could use more specific terms relevant for pri-miRNAs (e.g. GO:1902893 regulation of pri-miRNA transcription from RNA polymerase II promoter) if there is evidence for that. Similarly, if there is evidence that the TF binds another TF, then we could use the TF binding term, but I wouldn't want to suggest that as a recommended term.

I will put all this together with the other guidelines and send them around to everyone again, then I'll find out where I need to put them on the GO wiki/website.

Thanks again, Rachael.

Original comment by: rachhuntley