gocentral
commented
19 years ago Logged In: YES user_id=436423
> name: Chromosome Breakage > -- I'm not sure if this should be a 'sensu Ciliophora' > term, given the generic name of the process
In most, maybe all, other contexts, chromosome breakage is not a normal, regulated occurrence. If no other organisms have any normal chromosome breakage processes, the term does not have to be 'sensu Ciliophora'; we can use a comment to point out that the term is not to be used for DNA damage or other abnormal situations.
> Obsoletions
This sounds reasonable. Could you suggest comments for the obsolete terms (see http://www.geneontology.org/GO.format.html\#comments)?
I'm a little confused by this passage: 'The definition of [GO:0035196] is broad enough to allow this term to be used as a synonym for the three obsoleted microRNA terms.'
Does this imply that GO:0010494, GO:0010495, and GO:0030198 should be merged with GO:0035196 rather than obsoleted? Or should the text strings be used as synonyms, or should the comments on the obsolete terms simply direct one to GO:0035196 (the last option would be fine, possibly the best).
Apart from these small things, this proposal looks fine. Do you plan to implement it yourself, or would you like us to do so?
midori
Original comment by: mah11
Hi,
This is Nick Stover from the Tetrahymena Genome DB again. We need to request one more set of terms for an active area of ciliate research.
A process related to RNA interference (RNAi) is used by the ciliate Tetrahymena to direct the excision of parts of its genome. In order to accommodate this aspect of ciliate biology, and to represent the commonalities known and expected among this and other RNAi-related processes, Im requesting the following changes to the ontology. If you would like to view a diagram of the existing relationships (only the affected/relevant terms) compared with these proposed changes, please visit: http://genetics.stanford.edu/~nick/pictures/RNAiGOTree.jpg and http://genetics.stanford.edu/~nick/pictures/ RNAiGOTreeProposed.jpg Review articles on this process and its relationship to others involving small RNAs can be found in PMID: 15196465 and PMID:
Additions
name: programmed_DNA_elimination namespace: process def: Removal of micronuclear-limited sequences, internal eliminated sequences (IES) and breakage eliminated sequences (BES), from the developing macronucleus (anlage) of a ciliate. relationship: is_a GO:0006139 : nucleobase, nucleoside, nucleotide and nucleic acid metabolism
name: scnRNA production namespace: process def: Cleavage of noncoding, double-stranded RNAs transcribed from the micronuclear genome to produce scnRNAs, small RNAs (~28 nucleotides) that direct the deletion of micronuclear-limited sequences from the developing macronuclear genome. relationship: part_of PROPOSED: Programmed DNA Elimination; is_a PROPOSED: dsRNA fragmentation
name: Chromosome Breakage namespace: process def: Regulated cleavage of the developing macronuclear genome at a limited number of chromosome breakage sites (CBS). The macronuclear destined segment (MDS) sequence adjacent to the CBS (or separated from it by a BES) receives a macronuclear telomere following chromosome breakage. relationship: part_of PROPOSED: Programmed DNA Elimination -- Im not sure if this should be a Sensu Ciliophora term, given the generic name of the process
name: dsRNA Fragmentation namespace: process def: Cleavage of double-stranded RNA molecules by an RNaseIII- family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function. relationship: is_a GO:0006396 : RNA processing
name: Small RNA-Mediated Chromatin Silencing namespace: process def: Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region." relationship: is_a GO:0006342 : chromatin silencing
Obsoletions
GO:0010194 : microRNA metabolism ( 1 gene annotated ) GO:0010195 : microRNA biosynthesis ( 1 gene annotated ) GO:0030918 : microRNA processing ( 0 genes annotated )
The definition and parentage of the term microRNA biosynthesis implies the assembly of microRNAs from either nucleotides or short (smaller than the miRNAs) RNA fragments, which is not suggested in the cited abstract (TAIR accession Publication: 501707121). The absence of small RNAs noted in this abstract is likely due instead to the inability to fragment larger precursor RNAs.
miRNA production from a primary transcript is known at the moment to include two steps: an initial cleavage of the primary RNA transcript to ~70 nt RNAs, then a second step to create the functional miRNAs (PMID: 15211354). I am unaware of intermediate steps in the production of siRNAs or scnRNAs. As the definition for GO:0035196:miRNA-mediated gene silencing, production of miRNAs is written, both steps are covered. The definition of this term is broad enough to allow this term to be used as a synonym for the three obsoleted microRNA terms.
id: GO:0010194 name: microRNA metabolism namespace: process def: "The chemical reactions and physical changes involving microRNA, a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity." [TAIR:sm] exact_synonym: "miRNA metabolism" [] is_a: GO:0016070
id: GO:0010195 name: microRNA biosynthesis namespace: process def: "The formation from simpler components of microRNA, a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity." [TAIR:sm] exact_synonym: "miRNA biosynthesis" [] is_a: GO:0009058 is_a: GO:0010194
id: GO:0030918 name: microRNA processing namespace: process def: "Any process involved in the conversion of a primary microRNA transcript into a mature microRNA molecule." [GO:mah ""] exact_synonym: "miRNA processing" [] is_a: GO:0006396 is_a: GO:0010194
id: GO:0035196 name: miRNA-mediated gene silencing, production of miRNAs namespace: process def: "Cleavage of stem-loop RNA precursors (pre-miRNAs) that are encoded within plant and animal genomes into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein." [PMID:15066283, PMID:15066275] exact_synonym: "microRNA-mediated gene silencing, production of microRNAs" [] is_a: GO:0010195 relationship: part_of GO:0035195
Altered Relationships:
Currently GO:0035196:miRNA-mediated gene silencing, production of miRNAs is a child term of GO:0010195:microRNA biosynthesis (to be obsoleted). I propose that it should be a child of PROPOSED: dsRNA fragmentation, along with GO:0030422:RNA interference, production of guide RNAs and PROPOSED: scnRNA production.
id: GO:0030422 name: RNA interference, production of guide RNAs namespace: process def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides." [PMID:11524674] is_a: GO:0016070 relationship: part_of GO:0016246
Definitions of other terms in the diagrams:
id: GO:0030423 name: RNA interference, targeting of mRNA for destruction namespace: process def: "The process by which small interfering RNAs target cognate mRNA molecules for degradation." [PMID:11524674] relationship: part_of GO:0016246
id: GO:0016246 name: RNA interference namespace: process Synonyms: RNAi def: The process by which double-stranded RNAs silence cognate genes.
id: GO:0035194 name: RNA-mediated gene silencing namespace: process def: "Gene inactivation (silencing) triggered by small RNAs." [PMID:15066283, PMID:15066275] is_a: GO:0016441
id: GO:0035195 name: miRNA-mediated gene silencing namespace: process def: "Down regulation of gene expression through the action of microRNAs (miRNAs). miRNAs are endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). They act as guides for the miRNA-induced silencing complex (miRISC) and primarily silence genes by blocking the translation of mRNA transcripts into protein." [PMID:15066283, PMID:15066275] exact_synonym: "microRNA-mediated gene silencing" [] is_a: GO:0035194
id: GO:0035197 name: siRNA binding namespace: function def: "Interacting selectively with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme." [PMID:15066283, PMID:15066275] exact_synonym: "small interfering RNA binding" [] is_a: GO:0003723
id: GO:0035198 name: miRNA binding namespace: function def: "Interacting selectively with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes." [PMID:15066283] exact_synonym: "microRNA binding" [] is_a: GO:0003723
id: GO:0006342 name: chromatin silencing alt_id: GO:0016440 namespace: process def: "Repression of transcription by conversion of large regions of DNA into an inaccessible state often called heterochromatin." [PMID:10219245] comment: Note that this process is the opposite of chromatin- mediated maintenance of transcription. This regulation is exemplified by members of the Polycomb group, which maintain the inactive state of homeotic gene transcription. synonym: "TGS" [] synonym: "heterochromatin formation" [] synonym: "transcriptional gene silencing" [] exact_synonym: "chromatin-mediated maintenance of transcriptional inactivation" [] exact_synonym: "chromatin-mediated silencing" [] is_a: GO:0006338 is_a: GO:0016458 is_a: GO:0045814 is_a: GO:0045892
id: GO:0016441 name: posttranscriptional gene silencing namespace: process def: "Posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and occurs through a specific decrease in the level of mRNA of both host genes and transgenes." [WB:ems, PMID:11713190] synonym: "quelling" [] exact_synonym: "PTGS" [] is_a: GO:0016458 is_a: GO:0040029 related_synonym: "cosuppression" []
id: GO:0035087 name: RNA interference, siRNA loading onto RISC namespace: process def: "The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC)." [PMID:14512631, FB:bf] relationship: part_of GO:0016246
Reported by: nastover
Original Ticket: "geneontology/ontology-requests/2047":https://sourceforge.net/p/geneontology/ontology-requests/2047