Open hattrill opened 2 years ago
Annotations are here: https://docs.google.com/spreadsheets/d/1og1_ZyWBl133-nZnJjXC4HnG5HfmjxmJt4HXWdpX2Kk/edit#gid=0
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:
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
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.
piRNA processing:
NTR? : TRANSPOSON SILENCING Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons
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.
Created some new terms
+[Term] +id: GO:0140891 +name: co-transcriptional transposon silencing +namespace: biological_process +def: "A heterochromatin formation-based transposon silencing process mediated by a small RNA molecule that occur concurrently with trancription. piRNAs and tRNAs are known to repress transposon transcription." [PMID:33789107] +synonym: "piRNA-mediated co-transcriptional transposon silencing" NARROW [] +synonym: "tRNA-mediated co-transcriptional transposon silencing" NARROW [] +is_a: GO:0031047 ! gene silencing by RNA +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23135 xsd:anyURI +created_by: pg +creation_date: 2022-07-19T14:47:36Z + +[Term] +id: GO:0140892 +name: post-transcriptional transposon silencing +namespace: biological_process +def: "A heterochromatin formation-based transposon silencing process mediated by a small RNA molecule that occur after trancription. piRNAs are known to repress transposon transcription post-transcriptionally." [PMID:33789107] +synonym: "piRNA-mediated post-transcriptional transposon silencing" NARROW [] +is_a: GO:0031047 ! gene silencing by RNA +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/23135 xsd:anyURI +created_by: pg +creation_date: 2022-07-19T14:47:36Z
@gantonazzo @hattrill I think these definitions can be improved, the explanation is not clear as to what is co- and what is post-transcriptional silencing.
Questions:
Additional task to review regulation of transposition https://docs.google.com/spreadsheets/d/1F_70d1hpogIfEoSiC-8FRvVy4HXCTwduJGBVhg8TOuY/edit#gid=0 Details on https://github.com/geneontology/go-ontology/issues/23135
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.
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
Useful description of piRNA - piwi complexes and their specificity in this article
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
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
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)
May have to have a Tertiary piRNA processing term for phased piRNA production but need more papers to get definition correct.
How is TE silencing and piRNA silencing related in GO and how can this be represented?
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)
https://www.tandfonline.com/doi/full/10.4161/worm.28234 c.elegans only have primary piRNA pathway
Well, that makes it easier!:)
Some Rules/giudes for annotation (add to this list) Note for primary processing
Note for secondary processing
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.
https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6601507&blobtype=pdf Nice diagram that explains localization of primary and secondary processing
making sure all components are covered.
see GO ticket go-ontology/issues/23135