Proposal for obsoleting "transcription, RNA dependent"

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Issue

The term transcription, RNA-dependent (GO:0006410) should be obsoleted because the name and the definition mean two completely different things:

  1. 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.
  2. 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).

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.

Done: 3/14/2011

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).

  1. 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)
  2. 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:

  1. move the term to be a child of the new term reverse transcription in the DNA replication tree
  2. 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

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