Review piRNA biogenesis annotations

[hattrill]

see GO ticket go-ontology/issues/23135

[hattrill]

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

• 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
• should GO:0034588 piRNA catabolic process be obsoleted?

[hattrill]

Notes on biogenesis from One Loop to Rule Them All:The Ping-Pong Cycle and piRNA-Guided Silencing

piRNA cluster: clustering of multiple piRNAs at distinct genomic loci, resulting in sites with high piRNA coverage. Cytologically, mouse clusters reside in euchromatic domains, whereas clusters in flies are embedded in heterochromatin and predominantly found at pericentromeric and subtelomeric regions.
piRNA clusters rarely contain full-length copies of transposons- they harbor remnants and nested fragments that are unable to transpose.
Dual-strand clusters produce piRNAs from both genomic strands by convergent transcription, as seen for most Drosophila germline clusters
Uni-strand’ clusters give rise to piRNAs from one genomic strand. Most meiotic piRNA clusters are considered uni-strand clusters, although they are transcribed from promoters that fire bidirectionally, because the produced piRNA are restricted to individual, nonoverlapping genomic strands.

Primary piRNA biogenesis can be broken down into several steps:

1. piRNA cluster transcripts generated
2. transcripts licensing to produce piRNA molecules
3. exported to the processing sites located in the cytoplasm
4. Cluster transcripts are cleaved into piRNA intermediates, which are then loaded into PIWI proteins and subsequently trimmed and methylated to yield mature piRNA-PIWI complexes.
   OR
   Zucchini-dependent 3' end formation of PIWI-associated piRNA intermediates can result in the production of trimming-independent, phased piRNAs.

Mature piRNA-PIWI complexes have different fates depending on the protein involved
-Drosophila Piwi will enter the nucleus
-Drosophila Aubergine (Aub), which is also loaded with primary piRNAs, localizes to the perinuclear cytoplasm

The localization of these Argonaute proteins influences the mode of action by which they carry out silencing

1. Transcriptional gene silencing (TGS). piRNA-directed TGS leads to target shutdown through chromatin modifications that include repressive histone marks and DNA methylation.
2. post-transcriptional gene silencing (PTGS).
   Typically, piRNA-mediated PTGS is sequence specific and depends on catalytically active enzymes. The ping-pong cycle, not only utilizes PTGS to destroy transposon mRNAs, but also harnesses this mechanism to amplify silencing triggers targeting active elements. In addition, the concomitant production of phased piRNAs allows sequence diversification via spreading and feeds back to TGS-competent PIWI proteins.

[hattrill]

• New Terms for transcription of piRNAs

Legend: The body of uni-strand piRNA clusters carries repressive H3K9me3 marks. Yet, clusters resemble coding genes in that their promoters contain H3K4me2 marks. piRNA clusters also produce transcripts via RNA PolII that have caps, undergo (alternative) splicing and are terminated by canonical poly(A) signals. Meiotic piRNA clusters show similar characteristics, yet often produce piRNAs from two non-overlapping genomic strands. These clusters are transcribed from bidirectional promoters that are activated by the Myb transcription factor. Dual-strand clusters in Drosophila germ cells carry H3K9me3 modifications, but show no H3K4me2 signatures typical for active promoters. These piRNA clusters utilize Pol II-dependent, non-canonical read-through transcription from neighboring coding genes. It is hypothesized that 3' end processing of the nascent RNAs results in the release of uncapped piRNA precursors. Cutoff (Cuff), a component of the Rhino-Deadlock-Cutoff complex that is anchored on piRNA cluster bodies via the H3K9me3-binding capacity of Rhi, associates with these uncapped transcripts and protects them from degradation, splicing, and transcription termination.

use piRNA trancription GO:0140541 for both these processes, could use anti-termination terms in conjunction or locus info to capture factor/cluster-specific processes.

[hattrill]

• Merge GO:1990511 piRNA biosynthetic process into GO:0034587 piRNA metabolic process.
• Move annotations under piRNA biosynthetic process that should be associated with piRNA transcription
• Add piRNA processing terms under small regulatory ncRNA processing
• new terms for ping-pong amplification?
  

[hattrill]

Other refs:

• PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond

• Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways

• The piRNA pathway in Drosophila ovarian germ and somatic cells

[hattrill]

piRNA processing:

[hattrill]

NTR? : TRANSPOSON SILENCING Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons

[gantonazzo]

I think that would make sense. piRNAs act via transposon silencing and if tRNAs also act on transposons, then it would make sense to have the new term as a common parent, I think.

[hattrill]

Additional task to review regulation of transposition https://docs.google.com/spreadsheets/d/1F_70d1hpogIfEoSiC-8FRvVy4HXCTwduJGBVhg8TOuY/edit#gid=0
Details on geneontology/go-ontology#23135

[hattrill]

Sheet with papers for curation for biogenesis

[hattrill]

Fly piRNA biogenesis: tap dancing with Tej looks at the difference between where primary and secondary processing occurs:

In short, primary and secondary processing are separate processes.

[hattrill]

Note: came across these terms:
GO:1990471 piRNA uni-strand cluster binding
GO:1990472 piRNA dual-strand cluster binding
which would be useful to review

[hattrill]

Useful description of piRNA - piwi complexes and their specificity in this article

[hattrill]

Draft definition for primary piRNA processing

The process involved in converting precursor piRNAs (long single-stranded capped and polyadenylated RNAs) 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

Might change the def to remove mention of U as in mouse this preference might not be so strong - need to check (https://www.science.org/doi/10.1126/science.aaa1039) .....Update, U bias ok for mice too https://www.nature.com/articles/cr2012120

[hattrill]

From PMID: 19270082

"The third class of small RNAs appears to be specific to animals and interacts with an animal-specific clade of Argonaute proteins, the Piwi family (Aravin et al. 2007a). These Piwi-interacting RNAs (piRNAs) have been found in Caenorhabditis elegans (Batista et al. 2008; Das et al. 2008), Drosophila (Saito et al. 2006; Brennecke et al. 2007), zebra fish (Houwing et al. 2007, 2008), and mam- mals (Aravin et al. 2006, 2007b; Girard et al. 2006; Grivna et al. 2006; Lau et al. 2006; Watanabe et al. 2006), where their expression is most prominent in male and female germ cells. In most organisms, piRNAs have clear roles in guarding germ cell genomes from the activity of mobile genetic elements ...."

Taxon restriction for all piRNA terms should be:
Only in Metazoa.
Taxonomy ID:33208

[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 MILI and MIWI2.
PMID:32895365
PMID:29281264

Note: official name of MIWI2 is Piwil4 and MILI is Piwil2 (http://www.informatics.jax.org/marker/MGI:1930036)

[hattrill]

May have to have a Tertiary piRNA processing term for phased piRNA production but need more papers to get definition correct.

[hattrill]

How is TE silencing and piRNA silencing related in GO and how can this be represented?

[hattrill]

From DOI: 10.1111/raq.12557
Dmel vs mouse vs fish (note that they don't really go into dual strand clusters, so the secondary is not all that correct)

[hattrill]

https://www.tandfonline.com/doi/full/10.4161/worm.28234
c.elegans only have primary piRNA pathway

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015490/

[gantonazzo]

Well, that makes it easier!:)

[hattrill]

Some Rules/giudes for annotation (add to this list)
Note for primary processing

• In flies and mice, primary piRNAs derive from piRNA clusters transcribed as single-stranded transcripts. In C.elegans piRNAs are produced from single piRNA transcripts and so primary processing is limited to piRNA modification and trimming. (PMID: 26919432)
• The targets of primary processing are generally single-stranded pre-piRNA derived from one strand (unistrand). They are polyadenylated and capped in the cononical nuclear RNA processing pathway.

Note for secondary processing

• The targets of secondary processing are from bi-directional transcription of the template (dual strand). In D.mel, dual-strand piRNA clusters do not possess their own promoters and are regulated by non-canonical transcriptional mechanisms driven by Rhino, Deadlock and Cutoff. These transcripts are not polyadenylated or capped.
• In secondary processing, destruction of the target mRNA is coupled to the amplification of piRNAs.

[hattrill]

Hi @pgaudet 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.

[hattrill]

https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6601507&blobtype=pdf
Nice diagram that explains localization of primary and secondary processing

[hattrill]

https://docs.google.com/spreadsheets/d/1J6UDUIoQwvCngBJ0eNNQwGlgIMLHkNLJIzK4dy18Ono/edit#gid=1735865106

making sure all components are covered.