Proposal for obsoleting "transcription, RNA dependent"
Issue
The term transcription, RNA-dependent (GO:0006410) should be obsoleted because the name and the definition mean two completely different things:
- transcription, RNA-dependent, i.e. RNA-dependent production of an RNA transcript.
- - There are a number of viruses that perform this type of RNA biosynthetic process.
- reverse transcription, i.e. RNA-dependent DNA synthesis.
- - The existing term transcription, RNA-dependent (GO:0006410) is defined as "The cellular synthesis of DNA on a template of RNA." and has reverse transcription as an EXACT synonym.
- - There is already a term RNA-dependent DNA replication (GO:0006278) that is more accurately placed in the graph and which has a definition intended to cover the synthesis of DNA from an RNA template. Note that it mentions reverse transcriptase as an example in the definition. It may have originally been intended to represent reverse transcription, but it now has a child term for telomere maintenance via telomerase (GO:0007004).
Proposal
A. We propose to create 2 new terms to represent the two new terms to represent the two distinct meanings of the existing term transcription, RNA-dependent (GO:0006410).
- transcription, RNA-dependent GO:new
- - Proposed Def: The cellular synthesis of RNA on a template of RNA.
- - Reuse of name: We propose to reuse the name transcription, RNA-dependent because it is parallel to the transcription, DNA-dependent name that is already in use for "normal" transcription. However, if people don't like reusing the name, we could call it RNA-dependent RNA transcript synthesis, or something similar.
- - parentage: is_a RNA biosynthetic process (GO:0032774)
- reverse transcription GO:new
- - Proposed Def: A DNA replication process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis. PMID: 20358252
- - parentage: RNA-dependent DNA replication (GO:0006278)
- Modifications to proposal based on discussion: In the definition of the new term for reverse transcription, we will use the phrase A DNA synthesis process instead of A DNA replication process.
B. Fate of transcription involved in RNA-mediated transposition (GO:0032199)
Currently transcription involved in RNA-mediated transposition (GO:0032199) is a child of transcription, RNA-dependent (GO:0006410). This is clearly a reverse transcription process based on the definition. We propose to:
- move the term to be a child of the new term reverse transcription in the DNA replication tree
- change the term name to reverse transcription involved in RNA-mediated transposition
Modifications to proposal based on discussion: Part C will not be acted upon now, but will deferred till later along with Part D. Please see the [SourceForge item for more information on the resolution of parts C & D].
C. issues with the term RNA-dependent DNA replication (GO:0006278)
This term is defined as "A DNA replication process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands." and looks like it has been used extensively for annotating reverse transcriptases.
We think that the definition should be revised to be more general, as befitting a grouping term with 2 types of RNA-dependent DNA replication processes under it.
Proposed new def: A DNA replication process that includes the use of RNA as a template for an RNA-dependent DNA polymerase, e.g. reverse transcriptase, telomerase.
As existing annotations are not wrong, just not as specific as they could be, we feel that there is no need to obsolete this term. Instead, once the new terms are in place, we would suggest reevaluation of existing annotations to see if they could be moved down to either the existing telomere maintenance via telomerase term or the new reverse transcription term.
D. This is a potential SF item, but not something that will be dealt with as part of the transcription overhaul. The definition of the term DNA replication (GO:0006260) seems specific to DNA-dependent DNA replication and possibly inappropriate as the parent term of RNA-dependent DNA replication. In addition, browsing via AmiGO suggests that DNA replication may suffer from the same annotation issue as transcription in that it is being used frequently when DNA-dependent replication is actually meant.
Many thanks to Harold Drabkin and Julie Park for their input on this issue
thanks,
-Karen & David
Comment Period
Date mailed: 2/21/2011
Deadline for Comments: 3/14/2011 - Unless objections are received by March 14, we will assume that you agree to this change.
Annotation Counts
Annotation counts of 6410 and other terms discussed, via AmiGO (Jan 2011):
GO:0006259 : DNA metabolic process [12366 gene products] - GO:0006260 : DNA replication [4609 gene products] -- GO:0006278 : RNA-dependent DNA replication [1040 gene products] --- GO:0007004 : telomere maintenance via telomerase [107 gene products] GO:0006350 : transcription [28093 gene products] - GO:0006410 : transcription, RNA-dependent [79 gene products] -- GO:0032199 : transcription involved in RNA-mediated transposition [0 gene products]
6410 Annotation counts, via GOOSE (2-17-2011):
GO:0006410 transcription, RNA-dependent PDB IEA 77 GO:0006410 transcription, RNA-dependent UniProtKB IDA 2 GO:0006410 transcription, RNA-dependent UniProtKB IEA 37618
6410 subsets, via GOOSE (2-17-2011):
GO:0006410 transcription, RNA-dependent Prokaryotic GO subset
6410 dbxrefs, via GOOSE (2-17-2011):
GO:0006410 transcription, RNA-dependent InterPro:IPR002527 GO:0006410 transcription, RNA-dependent InterPro:IPR008741 GO:0006410 transcription, RNA-dependent InterPro:IPR008742 GO:0006410 transcription, RNA-dependent InterPro:IPR013614 GO:0006410 transcription, RNA-dependent InterPro:IPR013648 GO:0006410 transcription, RNA-dependent InterPro:IPR013674 GO:0006410 transcription, RNA-dependent InterPro:IPR013707 GO:0006410 transcription, RNA-dependent InterPro:IPR014023 GO:0006410 transcription, RNA-dependent Pfam:PF01552 GO:0006410 transcription, RNA-dependent Pfam:PF05410 GO:0006410 transcription, RNA-dependent Pfam:PF05411 GO:0006410 transcription, RNA-dependent Pfam:PF08405 GO:0006410 transcription, RNA-dependent Pfam:PF08440 GO:0006410 transcription, RNA-dependent Pfam:PF08467 GO:0006410 transcription, RNA-dependent Pfam:PF08500 GO:0006410 transcription, RNA-dependent ProDom:PD649346 GO:0006410 transcription, RNA-dependent PROSITE:PS50526 GO:0006410 transcription, RNA-dependent SP_KW:KW-0693 GO:0006410 transcription, RNA-dependent Wikipedia:Reverse_transcription
Existing Term Stanzas
id: GO:0006410 name: transcription, RNA-dependent namespace: biological_process def: "The cellular synthesis of DNA on a template of RNA." [GOC:jl] subset: gosubset_prok synonym: "reverse transcription" EXACT [] xref: Wikipedia:Reverse_transcription is_a: GO:0006350 ! transcription id: GO:0006278 name: RNA-dependent DNA replication namespace: biological_process def: "A DNA replication process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands." [GOC:mah, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: gosubset_prok xref: Reactome:162589 "Reverse Transcription of HIV RNA" xref: Reactome:164516 "Minus-strand DNA synthesis" xref: Reactome:164525 "Plus-strand DNA synthesis" is_a: GO:0006260 ! DNA replication id: GO:0032199 name: transcription involved in RNA-mediated transposition namespace: biological_process def: "The synthesis of DNA from an RNA transposon intermediate." [GOC:jp, ISBN:1555812090] synonym: "reverse transcription during retrotransposition" EXACT [] is_a: GO:0006410 ! transcription, RNA-dependent intersection_of: GO:0006350 ! transcription intersection_of: part_of GO:0032197 ! transposition, RNA-mediated relationship: part_of GO:0032197 ! transposition, RNA-mediated id: GO:0006260 name: DNA replication namespace: biological_process alt_id: GO:0055133 def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah] comment: See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. subset: goslim_pir subset: goslim_pombe subset: gosubset_prok xref: Reactome:1006387 "Activation of ATR in response to replication stress" xref: Reactome:1014038 "Recruitment and activation of Chk1" xref: Reactome:1024839 "Activation of ATR in response to replication stress" xref: Reactome:1034782 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1034791 "Recruitment and activation of Chk1" xref: Reactome:1034793 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1034795 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1034812 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1034821 "Activation of claspin" xref: Reactome:1034822 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1051687 "Activation of ATR in response to replication stress" xref: Reactome:1061251 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1061263 "Recruitment and activation of Chk1" xref: Reactome:1061265 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1061267 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1061287 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1061303 "Activation of claspin" xref: Reactome:1061304 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1076646 "Activation of ATR in response to replication stress" xref: Reactome:1084516 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1084525 "Recruitment and activation of Chk1" xref: Reactome:1084527 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1084529 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1084546 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1084555 "Activation of claspin" xref: Reactome:1084556 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1097164 "Activation of ATR in response to replication stress" xref: Reactome:1105191 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1105204 "Recruitment and activation of Chk1" xref: Reactome:1105206 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1105208 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1105221 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1105238 "Activation of claspin" xref: Reactome:1105239 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1116447 "Activation of ATR in response to replication stress" xref: Reactome:1125306 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1125315 "Recruitment and activation of Chk1" xref: Reactome:1125317 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1125319 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1125340 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1125349 "Activation of claspin" xref: Reactome:1125350 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1140267 "Activation of ATR in response to replication stress" xref: Reactome:1152635 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:1152644 "Recruitment and activation of Chk1" xref: Reactome:1152646 "Stalling of DNA replication fork and RPA binding" xref: Reactome:1152648 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:1152673 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1152682 "Activation of claspin" xref: Reactome:1152683 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1170512 "Activation of ATR in response to replication stress" xref: Reactome:1180520 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1180530 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:1192340 "Activation of ATR in response to replication stress" xref: Reactome:1199348 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1206873 "Activation of ATR in response to replication stress" xref: Reactome:1243758 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1247047 "Activation of ATR in response to replication stress" xref: Reactome:1252489 "Activation of ATR in response to replication stress" xref: Reactome:1256317 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:1258281 "Activation of ATR in response to replication stress" xref: Reactome:176101 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:176116 "Recruitment and activation of Chk1" xref: Reactome:176175 "Stalling of DNA replication fork and RPA binding" xref: Reactome:176187 "Activation of ATR in response to replication stress" xref: Reactome:176250 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:176264 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:176298 "Activation of claspin" xref: Reactome:176318 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:963341 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:963350 "Recruitment and activation of Chk1" xref: Reactome:963352 "Stalling of DNA replication fork and RPA binding" xref: Reactome:963354 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:963374 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:963390 "Activation of claspin" xref: Reactome:963391 "Loading of claspin onto DNA during replication origin firing" xref: Reactome:979790 "Activation of ATR in response to replication stress" xref: Reactome:989857 "Recruitment of Rad17-RFC complex to DNA" xref: Reactome:989866 "Recruitment and activation of Chk1" xref: Reactome:989868 "Stalling of DNA replication fork and RPA binding" xref: Reactome:989870 "Binding of ATR-ATRIP to the RPA-ssDNA complex" xref: Reactome:989894 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA" xref: Reactome:989903 "Activation of claspin" xref: Reactome:989904 "Loading of claspin onto DNA during replication origin firing" xref: Wikipedia:DNA_replication is_a: GO:0006259 ! DNA metabolic process is_a: GO:0034645 ! cellular macromolecule biosynthetic process relationship: has_part GO:0071897 ! DNA biosynthetic process