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Source ontology files for the Gene Ontology
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NTRs: zygotic genome activation & maternal mRNA clearance #23918

Closed krchristie closed 1 year ago

krchristie commented 2 years ago

In the previous ticket, NTR: [Maternal-to-zygotic transition] #22659 , where the term "maternal-to-zygotic transition of gene expression" was created, @raymond91125 said:

It seems to me that to avoid confusion, we are probably better off to make MZT, MBT, and ZGA all distinct. From PMID19204068: "The stage at which maternal reliance ends and control of embryo development is transferred to the zygotic genome is referred to as the MZT. The MZT, under this definition, is distinct from the stage of zygotic genome activation (ZGA), which corresponds to the onset of de novo transcription from the zygotic genome. ZGA and MZT can coincide, but this is not always the case (Table1). The MZT is also distinct from the midblastula transition (MBT), a developmental transition in amphibians and fishes associated with cell cycle lengthening, asynchronous cleavage, and the acquisition of cell motility, which, however, does not require zygotic tran scription (Newport and Kirschner1982a). The distinction is not always clear in the literature, and the MBT and ZGA are often referred to as marking the MZT, although this is clearly not true in all organisms. In this review, we adhere to a strict distinction as defined above."

I'm currently working on this paper where Kmt2b (aka Mll2) is described as being involved in zygotic genome activation (ZGA):

Andreu-Vieyra CV, et al. 2010. MLL2 is required in oocytes for bulk histone 3 lysine 4 trimethylation and transcriptional silencing. PLoS Biol. 2010 Aug 17; 8(8):e1000453. doi:10.1371/journal.pbio.1000453. PMID:20808952

The current experimental annotations to the term "maternal-to-zygotic transition of gene expression" was created are from a paper which describes the role of Pabpn1l and Btg4 in maternal mRNA clearance: Zhao LW, Zhu YZ, Chen H, Wu YW, Pi SB,

Chen L, Shen L, Fan HY. PABPN1L mediates cytoplasmic mRNA decay as a placeholder during the maternal-to-zygotic transition. EMBO Rep. 2020 Aug 5;21(8):e49956. doi:10.15252/embr.201949956. Epub 2020 Jun 17. PMID: 32558204

Reading the same review @raymond91125 quoted in the previous ticket and both of the two papers cited above, I think we need two child terms of "maternal-to-zygotic transition of gene expression", both "zygotic genome activation" and "maternal mRNA clearance"

term: "zygotic genome activation" def: Any process that contributes to the onset of de novo transcription from the zygotic genome as part of the maternal-to-zygote transition in gene expression. ref: PMID:19204068, PMID:20808952 related_synonym: ZGA Cross-references: - parent_term: maternal-to-zygotic transition of gene expression Gene product name and ID to be annotated to this term: mouse Kmt2b (aka Mll2)

term: "maternal mRNA clearance" def: Any process that contributes to the clearance of maternal mRNA transcripts from the zygote as part of the maternal-to-zygote transition in gene expression. ref: PMID:19204068, PMID:32558204 exact_synonym: maternal mRNA degradation exact_synonym: maternal transcript clearance exact_synonym: maternal transcript degradation Cross-references: - parent_term: maternal-to-zygotic transition of gene expression Gene product name and ID to be annotated to this term: move MGI's IMP annotations for Pabpn1l and Btg4 from the existing term maternal-to-zygotic transition of gene expression to this new term.

@ukemi & @raymond91125 - How does this proposal sound to you? I don't mind doing the work, but wanted to check in with you two.

raymond91125 commented 2 years ago

That seems correct to me. Thanks for doing it.

pgaudet commented 1 year ago

Hi @krchristie

Sorry about the delay. Colin and I are finally working in this area. Note that I have used other 'is_a' parent than your suggestions, since these processes seem to be 'part_of' maternal-to-zygotic transition of gene expression (not is_a). let me know if that doesn't work.

+[Term] +id: GO:0141064 +name: zygotic genome activation +namespace: biological_process +def: "A process that contributes to the onset of de novo transcription from the zygotic genome as part of the maternal-to-zygote transition in gene expression. The zygote overcomes the silencing that has been established. The cause of this silencing could be due to several factors: chromatin modifications leading to repression, or lack of adequate transcription machinery." [PMID:19204068, PMID:20808952] +synonym: "ZGA" BROAD [] +is_a: GO:0010628 ! positive regulation of gene expression +relationship: part_of GO:0160021 ! maternal-to-zygotic transition of gene expression +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23918" xsd:anyURI +created_by: pg +creation_date: 2023-06-09T14:42:09Z + +[Term] +id: GO:0141065 +name: maternal mRNA clearance +namespace: biological_process +def: "The chemical reactions and pathways resulting in the clearance of maternal mRNA transcripts from the zygote as part of the maternal-to-zygote transition in gene expression." [PMID:19204068, PMID:32558204] +synonym: "maternal mRNA degradation" EXACT [] +synonym: "maternal transcript clearance" EXACT [] +synonym: "maternal transcript degradation" EXACT [] +is_a: GO:0006402 ! mRNA catabolic process +relationship: part_of GO:0160021 ! maternal-to-zygotic transition of gene expression +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23918" xsd:anyURI +created_by: pg +creation_date: 2023-06-09T14:50:39Z

Thanks, Pascale