Merge GO:0034587 piRNA metabolic process & GO:1990511 piRNA biosynthetic process ?

[pgaudet]

Discussing with @hattrill

• [x] GO:0034587 piRNA metabolic process and GO:1990511 piRNA biosynthetic process seem to have been used interchangeably to mean 'piRNA processing' - we need to review annotations to make sure the merge is OK

Annotations are here: https://docs.google.com/spreadsheets/d/1og1_ZyWBl133-nZnJjXC4HnG5HfmjxmJt4HXWdpX2Kk/edit#gid=0

• [x] the term should be moved under 'GO:0070918 small regulatory non-coding RNA processing
• [x] GO:0034588 piRNA catabolic process should be obsoleted

[pgaudet]

• [ ] NTR ~transposon silencing by piRNA-directed DNA methylation~ -> transposon silencing by piRNA-directed heterochromatin formation

-> ++ transposon silencing by piRNA-directed transposon transcript destabilization (https://pubmed.ncbi.nlm.nih.gov/33419460/)

https://pubmed.ncbi.nlm.nih.gov/32674113/

[pgaudet]

• [ ] NTR piRNA-mediated transposon silencing
• [ ] NTR tRNA-mediated transposon silencing

https://pubmed.ncbi.nlm.nih.gov/33789107/

see https://github.com/geneontology/go-ontology/issues/24561

[gantonazzo]

see https://github.com/FlyBase/GO-curation/issues/23

[pgaudet]

NTR piRNA amplification loop PMID:23706823

[pgaudet]

Note that piRNA is mediated by polII (are there other polymerases than transcribe piRNAs?)

[pgaudet]

Dear all,

The proposal has been made to obsolete 'GO:0034588 piRNA catabolic process'. The reason for obsoletion is that there is not evidence that this process exists; ie that piRNAs are specifically degraded. There are no annotations or mappings to this term, this term is not present in any subsets.

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/23135

Thanks, Pascale

[pgaudet]

GO:1990511

• [x] Changed label piRNA biosynthetic process -> to piRNA processing

• [x] Changed definition

• old def: : "The chemical reactions and pathways resulting in the formation of piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv, PMID:24696457]

• new def: ~"Any process that results in the conversion of one or more primary piRNAs transcripts into one or more mature piRNA molecules. piRNAs, also known as Piwi-associated RNAs, are a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv, PMID:24696457]~ A process leading to the generation of a functional piRNA. piRNAs (Piwi-associated RNAs) are a class of 24- to 30-nucleotide RNAs derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.

@gantonazzo @hattrill let me know if you want to change the definition.

Thanks, Pascale

[pgaudet]

From https://pubmed.ncbi.nlm.nih.gov/34724117/

piRNAs can be categorized into primary piRNAs and secondary piRNAs based on their biogenesis pathways, which are principally distinguished by their mechanisms of 5′end formation.

Primary piRNAs are produced from long single-stranded RNA precursors that are synthesized from piRNA loci, and their 5′ends are produced during the fragmentation process, likely involving the MitoPLD endonuclease (or PLD6, which has a homolog “Zucchini” in Drosophila) located on mitochondrial outer membranes.

Secondary piRNAs are produced from piRNA-targeted transcripts, and their 5′ends are generated by the endonucleolytic activity of PIWI proteins, which cleaves between positions 10 and 11 of the base-pair complementary RNA target relative to the piRNA 5′end. These secondary piRNAs can target the primary piRNA precursor transcripts to generate more secondary piRNAs, resulting in a piRNA-specific “Ping-Pong” loop. This loop is believed to represent an adaptive immune response that enables piRNAs to silence TE transcripts post-transcriptionally, as the loop continues to produce TE piRNAs until the TE transcripts are diminished (Gunawardane et al. 2007; Brennecke et al. 2007).

[pgaudet]

@gantonazzo From my reading (see pasted text above, among other references), the ping-pong amplification is part of 'secondary piRNAs processing' ; should we create 'primary piRNA processing' and 'secondary piRNA processing' as children of piRNA processing, instead of 'ping-pong amplification', which is one of the steps of the pathway?

[ValWood]

NTR piRNA amplification loop seems an odd term. Positive feedback loops exist in all of the siRNA pathways (not to mention many other pathways, cell cycle regulation etc). It isn't something we have usually explicitly created a GO term for.

I agree it is a useful concept to but I am not sure that GO terms are the place. Perhaps it should be something that is represented in some way in the modelling process (down the line, once we have nailed rules for simple regulation)

[pgaudet]

Right, it would be 'Secondary piRNA processing', see my comment just above

[ValWood]

But this is the case for every siRNA pathway

This is PTGS:

If you make this split, you are breaking down a 'linear pathway" which includes amplification , for which we know all the MF steps , into two processes.

primary RNAs and secondary RNAs seem that they would be better modelled as inputs and outputs rather than processes? Otherwise, we would need initiation and amplification processes for PTGS, siRNA dependent heterochromatin assembly, and every other RNAi related pathway

[pgaudet]

Do all the small RNAs go through this amplification process? I thought the siRNAs did, but not the miRNAs.

I think we need to review that branch to make sure that the terms are not redundant (ie that the pathways being described really are different); right now you are right that these all seems to just have different outputs, we need to add more details to describe the pathways.

[ValWood]

I don't know about miRNAs, but all the pathways which use siRNA have an amplification step. We have never included this in a term before.

I think it is a good idea to begin with a list of the known pathways an how they differ. From my limited knowledge the main difference between piRNA and siRNA is dicer dependent and that piRNA are dicer independent (I was going to open a ticket about this also because the definitions don't adequately describe the differences).

[pgaudet]

from https://pubmed.ncbi.nlm.nih.gov/20687832/

[pgaudet]

Discussion with @RLovering @hattrill

• [ ] NTR primary piRNA processing

• [x] NTR secondary piRNA processing synonym: ping-pong derived piRNA EXCACT synonym: ping-pong amplification RELATED

[pgaudet]

Also, we need a MF for piRNA

[pgaudet]

Good review on piRNA biogenesis and mechanism of action in mouse, Drosophila and C. elegans: https://pubmed.ncbi.nlm.nih.gov/33419460/

[ValWood]

Right, there is not always an amplification step, but the ampification when it occurs is performed by RNA dependent RNA polymerase, and so it is a single-step (MF)? Is that correct? Or are there other amplification mechanisms?

[ValWood]

This split NTR primary piRNA processing NTR secondary piRNA processing

sort of works, except that the RNA-dependent RNA polymerase amplification MF isn't processing (processing is specifically producing a mature RNA molecule and the amplification step is copying it)

i.e RNA-dependent RNA polymerase activity is involved in siRNA production but NOT in siRNA processing

[ValWood]

The paper I am reading right now calls this process "production" not processing

PMID:15615848

Title | RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production.

In C. elegans, RRF-1 and EGO-1 are essential for secondary siRNA production from RNAi-targeted transcripts in somatic cells and germ-line development, respectively (11, 27),

[hattrill]

Sticking to piRNA, which is indep of RNA-dep RNA pol - ping-pong amplification couples piRNA processing to target destruction. (think I got a bit mixed up with dual strand cluster transcription and the mechanism of ping-pong amplification on the call earlier today):

https://pubmed.ncbi.nlm.nih.gov/26810602/

So, possibly need to think about how 2ndary processing and piRNA-mediated destruction of transposon RNA are linked

[ValWood]

Be aware that priRNA 3'-end processing (GO:1990431) already exists, which overlaps somewhat with NTR primary piRNA processing ( it is proably equivalent? ) The process of forming the mature 3' end of a priRNA molecule. Perhaps this could be repurposed?

[hattrill]

Hi @ValWood are priRNAs only in yeast? I shall have a look at this.

I think for the ping-pong cycle it may be impossible to separate the generation of new secondary piRNAs from the destruction of transposon RNA or other target RNAs. I think I need to understand whether the first piRNA has some sort of initiator activity. From what I can understand, it mainly depends on the target - if it is at the level of transcription/chromatin structure, then primary piRNAs are sufficient to dampen the element but if a transposon is being actively transcribed, the ping pong mechanism is an 'adaptive' response which allows the cell to generate a cascade of piRNAs from the target so that there are more and new piRNAs sequences that are complementary to the transposon. ie primary piRNA seqs are determined by the piRNA gene and secondary piRNAs sequences are independent of the piRNA gene and reflect the transposon.

Think I am starting to get my head around it, but will probably need more discussion. Going to try and understand if there is any difference between regulating transposition and regulation of transposon transcription later today. @RLovering this paper has a summary of the types of transposition.

[ValWood]

woah that is cnfusing. I was confusing pri and pi, but I think they are the same thing.

"We have previously identified priRNAs, a class of Dicer-independent small RNAs in fission yeast." which is exactly what a pri is isn't it?

In this paper the authors refer to these as primal small RNAs https://pubmed.ncbi.nlm.nih.gov/30397104/ so I think pri an pi are referring to the same thing? I will double check this....

Certainly the pombe priRNAs ae involved in the genome surveillance and transposon quelling, so I think they are largely the same. Some parts of the pathway are the same but some are different (Our amplification step probably uses RdRP which is absent in flies, but I haven't looked at this pathway in detail.

[hattrill]

This is very good 'Fly piRNA biogenesis: tap dancing with Tej' looks at the difference between where primary and secondary processing occurs - essentially shows that In short, primary and secondary processing are separate processes, but, I would say that secondary processing is not separable from post-transcritional transposon silencing.

[pgaudet]

Discussion ncRNA @hattrill @gantonazzo @RLovering

• [ ] piRNA processing: add RELATED synonym: primary piRNA processing
• [x] NTR: secondary piRNA processing
• synonym: ping-pong derived piRNA EXACT
• synonym: ping-pong amplification RELATED
• definition:

[pgaudet]

@hattrill and @gantonazzo will provide a definition and reference

• the definition should explain how the processing of primary and secondary piRNA processing are different (in terms of pathway/mechanism)
• start and end of these processes

I'll update the definitions with this info

[pgaudet]

+[Term] +id: GO:0140965 +name: secondary piRNA processing +namespace: biological_process +def: "A the processing of a non-coding RNA \n..." [] +synonym: "ping-pong amplification" RELATED [] +synonym: "ping-pong derived piRNA" EXACT [] +synonym: "secondary piRNA biogenesis" EXACT [] +synonym: "secondary PIWI-associated RNA processing" EXACT [] +is_a: GO:0070918 ! regulatory ncRNA processing +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23135 xsd:anyURI +creation_date: 2022-12-12T13:25:26Z

(note that the definition is incomplete)

Maybe add comment that this has been characterized in insect and mouse

[pgaudet]

+[Term] +id: GO:0140966 +name: piRNA-directed heterochromatin formation +namespace: biological_process +namespace: The formation of facultative heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering piRNA. {comment="PMID:23329111"} +synonym: "piwiRNA-directed heterochromatin formation" EXACT [] +is_a: GO:0031048 ! RNA-mediated heterochromatin formation +created_by: pg +creation_date: 2022-12-12T13:51:08Z +

[pgaudet]

• [ ] NTR piRNA-mediated gene silencing by mRNA destabilization PMID:29281264

[pgaudet]

Draft definition for primary piRNA processing (from @hattrill in https://github.com/FlyBase/GO-curation/issues/23)

The process involved in converting precursor piRNAs into non-overlapping, contiguous primary piRNAs (∼24-30-nt piRNAs with a preference for a 5' uridine (U) via the endonucleolytic activity of cytosolic PIWI. This may include pre-piRNA maturation of 3′ ends by trimming and 2′-O-methylation.

Refs: PMID:34469728 PMID:26166577 PMID: 22907665

(note: removed ref to polyA and capping as not true of dual strand cluster derived piRNAs)

[hattrill]

Draft for "Secondary piRNA processing" A self-perpetuating piRNA loop, often called the ping-pong cycle, in which piRNAs are amplified by pairing with complementary transcripts (for example the transposable element mRNA target). In Drosophila, the processing involves the piwi proteins aubergine and Argonaute 3 and in mice, the piwi proteins Piwil2 and Piwil4. PMID:32895365 PMID:29281264

[hattrill]

We would like primary piRNA processing and secondary piRNA processing (synonyms: ping-pong piRNA processing, ping-pong amplification)

to be child terms of GO:0034587 piRNA processing (as this has been used for both primary and secondary)

All of these terms should be "Only in Metazoa TAXID:33208"

[hattrill]

We may also want "tertiary piRNA processimg" which can occur after primary or secondary pathways and is sometimes called phasing, but we will need to do a bit more background.

[hattrill]

+[Term] +id: GO:0140966 +name: piRNA-directed heterochromatin formation +namespace: biological_process +namespace: The formation of facultative heterochromatin into a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering piRNA. {comment="PMID:23329111"} +synonym: "piwiRNA-directed heterochromatin formation" EXACT [] +is_a: GO:0031048 ! RNA-mediated heterochromatin formation +created_by: pg +creation_date: 2022-12-12T13:51:08Z +

Hi @pgaudet I think that we decided not to use "facultative" here?

[pgaudet]

Hi @hattrill I removed 'facultative' from the definition.

A question for @colinlog - is H3K9me any heterochromatin, or facultative ?

Thanks, Pascale

[pgaudet]

We would like primary piRNA processing secondary piRNA processing to be child terms of GO:0034587 piRNA processing (as this has been used for both primary and secondary)

Should we not rather re-annotate ? (83 EXP). Or at least I will make 'piRNA processing' 'do not annotate'

[pgaudet]

Secondary piRNA processing draft definition: https://github.com/geneontology/go-ontology/issues/23135#issuecomment-1351273759

• [x] Added as "A process leading to the generation of a functional secondary piRNA, involving a self-perpetuating piRNA loop, often called the ping-pong cycle, in which piRNAs are amplified by pairing with complementary transcripts (for example the transposable element mRNA target). In Drosophila, the processing involves the piwi proteins aubergine and Argonaute 3 and in mice, the piwi proteins Piwil2 and Piwil4."

[colinlog]

H3K9me3 is any heterochromatin, including constitutive heterochromatin, but not every heterochromatin. H3K27me3 is facultative, mostly. There are about as many sites that have both H3K27me3 and H3K9me3, as there are with only any one of the two marks.

On Wed, Dec 14, 2022 at 2:47 PM pgaudet @.***> wrote:

Hi @hattrill https://github.com/hattrill I removed 'facultative' from the definition.

A question for @colinlog https://github.com/colinlog - is H3K9me any heterochromatin, or facultative ?

Thanks, Pascale

— Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/23135#issuecomment-1351386629, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALZVLKFEIGQLE2TM3VYSSJLWNHFWLANCNFSM5SPR4SQQ . You are receiving this because you were mentioned.Message ID: @.***>

[hattrill]

Should we not rather re-annotate ? (83 EXP). Or at least I will make 'piRNA processing' 'do not annotate'

It would be nice if people would do a review, but I would hestitate at making it a 'do not annotate'. I haven't quite got the feel of whether phased processing is better included as a primary processed or be a separate 'tertiary' process, my feeling is for the former as it seems like a relatively normal part of processing piRNAs from repeats.

[hattrill]

Draft def for piRNA-mediated gene silencing by mRNA destabilization

A cytoplasmic post-transcriptional gene silencing pathway in which piRNAs direct the cleavage of target mRNAs. The target mRNA, often transcribed from a transposable element, is destabilized by the activity of a PIWI class endonuclease within the piRNA-induced silencing complex. This may also be accompanied by mRNA deadenylation and decapping. PMID:33419460 PMID:29281264

[hattrill]

Hi @pgaudet, just got round to reviewing this ticket: piRNA processing still needs some work:

1. piRNA processing GO:0034587 - definition is fine

2. Secondary piRNA processing GO:0140965 - definition is fine ; should be a child of piRNA processing GO:0034587 rather than ncRNA processing GO:0034470

3. need to add new term: primary piRNA processing Def "The process involved in converting precursor piRNAs into non-overlapping, contiguous primary piRNAs (∼24-30-nt piRNAs with a preference for a 5' uridine (U) via the endonucleolytic activity of cytosolic PIWI. This may include pre-piRNA maturation of 3′ ends by trimming and 2′-O-methylation.""

Refs: PMID:34469728 PMID:26166577 PMID: 22907665

Make child of piRNA processing GO:0034587

[hattrill]

For the 'silencing':

1. piRNA-directed heterochromatin formation GO:0140966 - looks done

2. Term still to make: piRNA-mediated gene silencing by mRNA destabilization

A cytoplasmic post-transcriptional gene silencing pathway in which piRNAs direct the cleavage of target mRNAs. The target mRNA, often transcribed from a transposable element, is destabilized by the activity of a PIWI class endonuclease within the piRNA-induced silencing complex. This may also be accompanied by mRNA deadenylation and decapping. PMID:33419460 PMID:29281264

Not sure if we discussed the parentage of this? As, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8490990/ says "piRNAs execute transposon repression in two ways: degrading their RNA transcripts and compacting the genomic loci via heterochromatinization"

think that this can be a child of both:

mRNA destabilization GO:0061157 and RNA-mediated post-transcriptional gene silencing GO:0035194

[pgaudet]

@hattrill There are 83 EXP to piRNA processing: https://docs.google.com/spreadsheets/d/1HY8e48mwjpQRyl37S6pjGsfiGG_PGwV73C2Kosb1iOg/edit#gid=0

Could we rehouse them under primary or secondary? Or are there cases where we cannot tell which it is ?

[pgaudet]

From https://github.com/FlyBase/GO-curation/issues/23#issuecomment-1410007885

@hattrill commented

I think from looking over the papers Giulia and I think that it would be safer to have a parent term (piRNA processing) for primary piRNA processing or secondary terms. The reasoning behind this is that although they can be and mainly are separate processes, there are examples where they may feed into each other or that authors are just not clear. And, if we were to make a term for tertiary processing (and I am not sure about whether we would want that), it would have to be under a generic parent as it can't take place without primary or secondary processing first.

[pgaudet]

+[Term] +id: GO:0140990 +name: primary piRNA processing +namespace: biological_process +def: "The process involved in converting precursor piRNAs into non-overlapping, contiguous primary piRNAs (approximately 24-30-nt piRNAs with a preference for a 5' uridine (U) via the endonucleolytic activity of cytosolic PIWI. This may include pre-piRNA maturation of 3' ends by trimming and 2'-O-methylation." [PMID:22907665, PMID:26166577, PMID:34469728] +is_a: GO:0034587 ! piRNA processing +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23135 xsd:anyURI +created_by: pg +creation_date: 2023-02-01T13:36:56Z

[pgaudet]

+[Term] +id: GO:0140991 +name: piRNA-mediated gene silencing by mRNA destabilization +namespace: biological_process +def: "A cytoplasmic post-transcriptional gene silencing pathway in which piRNAs direct the cleavage of target mRNAs. The target mRNA, often transcribed from a transposable element, is destabilized by the activity of a PIWI class endonuclease within the piRNA-induced silencing complex. This may also be accompanied by mRNA deadenylation and decapping." [PMID:29281264, PMID:33419460] +is_a: GO:0035194 ! ncRNA-mediated post-transcriptional gene silencing +is_a: GO:0061157 ! mRNA destabilization +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23135 xsd:anyURI +created_by: pg +creation_date: 2023-02-01T13:56:48Z

[pgaudet]

I created a ticket to reanotate to the more precise terms when possible: https://github.com/geneontology/go-annotation/issues/4432

I think this takes care of all tasks in the present ticket.

Closing.

[pgaudet]

• [ ] primary piRNA processing and secondary piRNA processing Add TC "Only in Metazoa TAXID:33208"