Difference between revisions of "RNA processing"

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(May 25th, 2007 session)
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'''Next meeting:''' June 1st at 10 am  Pacific
 
'''Next meeting:''' June 1st at 10 am  Pacific
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 +
 +
== June 1st, 2007 session ==
 +
 +
'''Present''': Harold Drabkin, Karen Christie, Ceri Van Slyke
 +
 +
'''Discussion:'''
 +
 +
We discussed the child terms for the two new maturation terms Harold had put in for maturation of bacterial SSU and LSU rRNAs and changed some of the relationships so that an given step can be made a child of a 'maturation of LSU' or 'maturation of SSU' term, rather than all endonucleolytic cleavages of the bacterial pre-rRNA txpt automatically being children of both of these maturation terms. We also removed the specific reference to 'by RNase III' from these defs so that these terms will not be too narrow if other bacteria with the same txpt organization use something other than RNase III.
 +
 +
In response to last week's edits Midori had sent some comments by email, copied below, so we went through Midori's email and made the suggested corrections.
 +
 +
<pre>
 +
Date: Wed, 30 May 2007 14:42:42 +0100 (BST)
 +
From: Midori Harris <midori@ebi.ac.uk>
 +
To: Karen Christie <kchris@genome.stanford.edu>
 +
Cc: Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>, Harold Drabkin <hjd@informatics.jax.org>
 +
Subject: Re: rRNA processing stuff
 +
 +
Hi,
 +
 +
This has realy come a long way -- I'm impressed. Thanks for all the work you're putting in!
 +
 +
I like the latest idea (below and in RNA-alt.obo) for dealing with rRNA 3'-end processing
 +
 +
The proposal to obsolete GO:0030489 sounds reasonable. I recommend sending the usual "Alert" email with the
 +
two-week notice period, so we can honestly say we're following procedure.
 +
 +
A few more small things:
 +
 +
Merging '35S primary transcript processing' (GO:0006365; typo on wiki) into rRNA processing looks good, although
 +
I wonder if the synonym scope for the "35S processing" string should be  narrow -- are there any primary
 +
transcripts of different sedimentation coefficient? (If not, the synonym can stay exact.)
 +
 +
I presume the defs will be filled in for GO:000459, 461, 462 and 464-469 -- Karen's to-do #1?
 +
 +
Missing 'S' in GO:0000460 def.
 +
 +
It might be worth saying what 'ETS' stands for in the GO:0000446 def.
 +
 +
I'll try to make a brief appearance at the Friday chat, but since it starts at 6pm UK time I probably won't stay
 +
for the whole thing (also - the invite I got says 10 PM, not am). It will be great to have this go live.
 +
 +
cheers,
 +
midori
 +
</pre>
 +
 +
'''To do List for next time:'''
 +
*Karen
 +
*# def for GO:0000469 (missed this one last week)
 +
*# check where "cleavage at C2" synonym belongs (currently on 2 terms)
 +
*# check Archaeal
 +
* Everyone check over the whole file for
 +
*# general logic
 +
*# defs, correctness, typos, etc.
 +
*# residual comments, make sure we don't still have any comments to ourselves which should not become public
 +
 +
Karen will make today’s edits available on the ftp site for Harold, Ceri, and MIdori to look at on. It is here:
 +
 +
ftp://genome-ftp.stanford.edu/pub/people/curator/gene_ontology_edit-rRNA-20070601.obo
 +
 +
'''Summary'''
 +
 +
We think we are just about done with this. So we have not scheduled another meeting. Instead, all 3 of us, and MIdori if interested, will go through all the terms, defs, comments, synonyms, etc. to see if we've missed anything. The deadline for comments is '''June 7th'''. If we find anything that prevents proceding, we plan to send out an email about the proposed obsoletion of GO:0030489 (27S rRNA processing) on June 11th and can then make the changes on June 25, assuming no one objects to the obsoletion.

Revision as of 11:19, 1 June 2007

Formation of group and scope of issue

Date: Wed, 28 Feb 2007 15:31:08 +0000 (GMT)
From: Midori Harris <midori@ebi.ac.uk>
To: Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>, Karen Christie <kchris@genome.stanford.edu>,
    Harold Drabkin <hjd@informatics.jax.org>
Cc: David Hill <dph@informatics.jax.org>
Subject: RNA processing

Hi,

As part of our campaign to get a grip on the outstanding SourceForge items, I'd like to assemble a task
force to deal with the RNA processing term definitions once and for all. We have three open items, two
of which have been hanging around for an embarrassingly long time:

https://sourceforge.net/tracker/?func=detail&aid=780275&group_id=36855&atid=440764
https://sourceforge.net/tracker/?func=detail&aid=1067017&group_id=36855&atid=440764
https://sourceforge.net/tracker/?func=detail&aid=1566692&group_id=36855&atid=440764

Karen, Harold and Ceri -- from the SF comments I've formed the impression that you would be able to
contribute to this effort. Would you be willing to participate in a web conference to work on the terms
and definitions? And can you think of anyone else who should be involved? Finally, are there any dates
and times that are particularly good or bad for you?

I don't consider myself anything like an expert on this subject, but I'm willing to participate in the
working session from a general GO perspective.

Many thanks,
Midori (and David)

March 26, 2007 session

Present: Midori Harris, Harold Drabkin, Karen Christie, Ceri Van Slyke

mostly working out the kinks of Webex and Skype and defining scope of issue to tackle, i.e. rRNA processing terms in the Process ontology

To Do list:

  1. Karen:
    • nuclear in fungi
    • mitochondrial in fungi
    • in archaea
  2. Harold:
    • nuclear in mammals
    • mitochondrial in mammals
    • in bacteria
  3. Ceri, would you be able to check into rRNA processing in your organism.
  4. We also need to check into plants, and there are potentially three things that need to be checked:
    • nuclear
    • mitochondrial
    • chloroplast

April 2nd, 2007 session

Present: Harold Drabkin, Karen Christie, Ceri Van Slyke

Proposed ideas for ontology structure:

rRNA processing
..endonucleolytic cleavages *K
....cleavage of  tricistronic rRNA transcript (SSU-5.8S-LSU) *K
......cleavage of  5’ETS *K
......cleavage between SSU.rRNA and 5.8S-LSU *K
......cleavage between 5.8S and LSU *K
....cleavage of  tricistronic rRNA transcript (SSU-LSU-5S) *H
......cleavage between SSU and LSU *H
......cleavage between LSU and 5S *H
....cleavage of bicistronic rRNA transcript (SSU-LSU) *K
......cleavage between SSU and LSU *K
....cleavage of  monocistronic primary LSU rRNA transcript *K
....cleavage of  monocistronic primary SSU rRNA transcript *K

..exonucleolytic trimming

.rRNA modification (existing) *C and below (make this an is_a child of rRNA processing)
..base modification
....pseudouridylation during ribosome biogenesis
......templated
......non-templated
....2’-O-methylation during ribosome biogenesis
......templated
......non-templated
....dimethylation during SSU biogenesis *H


*H = Harold to work on defs for these
*C = Ceri to work on defs for these
*K = Karen to work on defs for these

To Do list:

  1. Plants
    • nuclei - Karen
    • chloroplasts – Ceri
    • mitochondria – Harold
  2. Harold will flesh out exonucleolytic trimming steps
  3. Karen will incorporate today’s work into an obo-edit file
  4. also need to think about how to rephrase these two term defs:
    • non-guided rRNA 2’-O-methylation _The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule without using a guide RNA. (need to rephrase this to avoid a negation of the guided methylation term)
    • non-guided rRNA pseudouridine synthesis _The intramolecular conversion of uridine to pseudouridine with no guide RNA. (need to rephrase this to avoid a negation of the guided pseudouridylation term)
  5. Do we need to look into 5S processing???

April 9th, 2007 session

Present: Harold Drabkin, Karen Christie, Ceri Van Slyke

Based on the work, each of us had done earlier (Harold and Ceri sent word docs, Karen had worked in OBO-Edit), we discussed the various defs and suggested some changes to come up with this set of proposed definitions.

Proposed definitions:

rRNA modification_The covalent alteration of one or more nucleotides within an rRNA molecule,.

i--rRNA editing - The insertion, deletion or substitution of nucleotide residues within nascent rRNA transcripts to produce rRNA molecules with sequences that differ from those coded genetically. (how to distinguish this from methylation, pseudoU?)

i--rRNA methylation - The posttranscriptional addition of methyl groups to specific nucleotide residues in an rRNA molecule.

i---rRNA 2’-O-methylation - The posttranscriptional addition of a methyl group to the 2'-O atom of a nucleotide residue in an rRNA molecule (check F def for 2’-O-methylation)

i----snoRNA guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule using a snoRNA guide. (synonym: templated…???)

i----non-guided rRNA 2’-O-methylation - The posttranscriptional addition of methyl groups to the 2'-O atom of a nucleotide residue in an rRNA molecule without using a guide RNA. (need to rephrase this to avoid a negation of the guided methylation term)

i--rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.

i--- snoRNA guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine in an rRNA molecule using a snoRNA guide.

i--- non-guided rRNA pseudouridine synthesis - The intramolecular conversion of uridine to pseudouridine with no guide RNA. (need to rephrase this to avoid a negation of the guided pseudouridylation term)

i----dimethylation during SSU-rRNA biogenesis - The process of di-methyation of the N6 of two consecutive adenosine residues near the 3'-end of the SSU rRNA. This process has been conserved in evolution from bacteria to eukaryotes.

To Do list:

  1. Karen to put all work into an OBO-Edit file and send it to Harold & Ceri
  2. To continue to work on previously agreed areas

April 17th, 2007 session

Present: Harold Drabkin, Ceri Van Slyke

We added Ceri's terms on vascular plant rRNA endonucleolytic cleavages.

From what she has seen for algae, we perhaps can add to the tricistronic processing (ssu-lsu-5s) a note about also seen in algal mito rRNA

Harold mailed the new obo file to Karen

May 18th, 2007 Session

Present: Karen Christie, Harold Drabkin, Ceri Van Slyke

Prior to the meeting, there was an exchange of emails:

from Karen:

Date: Mon, 7 May 2007 14:48:46 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: Karen Christie <kchris@genome.stanford.edu>
Cc: Harold Drabkin <hjd@informatics.jax.org>, Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>
Subject: next meeting for rRNA processing?

Hi,

I also have a question about this term and its children:

"endonucleolytic cleaveage of tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)"

The def of this term:

"endonucleolytic cleaveage between SSU-rRNA and LSU-rRNA of polycistronic rRNA transcript (SSU-rRNA,
LSU-rRNA, 4.5S-rRNA, 5S-rRNA)"

includes the sentence:

"These cleavages liberate tRNAs from the polycistronic transcript as well as separating the SSU and LSU
containing transcript."

Thus I was wondering if it's a misnomer to call this a 'tetracistronic ... transcript' since it contains
more than 4 things. It also seems like it might be confusing to not mention the tRNA in the defs for the
other 3 related terms, but only in this one. Are there some chloroplasts where there is a tRNA and others
where there isn't? Anyway, I think we might need to revisit this a bit.

cheers,

-Karen

Ceri responded with this info:

Date: Mon, 07 May 2007 16:09:47 -0700
From: Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>
To: Karen Christie <kchris@genome.stanford.edu>
Cc: harold Drabkin <hjd@informatics.jax.org>
Subject: Re: next meeting for rRNA processing?
Parts/Attachments:
   1   OK     98 lines  Text
   2 Shown    86 lines  Text
----------------------------------------

At 02:48 PM 5/7/2007, you wrote:
      The def of this term:

      "endonucleolytic cleaveage between SSU-rRNA and LSU-rRNA of polycistronic rRNA
      transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA)"


I think I missed an edit here.

      includes the sentence:

      "These cleavages liberate tRNAs from the polycistronic transcript as well as
      separating the SSU and LSU containing transcript."


This was to be a note or comment.


      Thus I was wondering if it's a misnomer to call this a 'tetracistronic ... transcript'
      since it contains more than 4 things. It also seems like it might be confusing to not
      mention the tRNA in the defs for the other 3 related terms, but only in this one. Are
      there some chloroplasts where there is a tRNA and others where there isn't? Anyway, I
      think we might need to revisit this a bit.

We call the prokaryote arrangement of  genes tricistronic and don't mention the tRNAs in the
transcript (they range from 0-3, maybe more PMID: 16980415, PMID: 12533472-FIG4 ).   I think all
the known transcripts of chloroplast rRNAs have at least one tRNA or pseudotRNA ( PMID: 1600142,
PMID: 15926220 ), however the number of tRNAs varies between known species.   Chloroplast in green
algae have 2-3 tRNAs in their rRNA operon, with a gene order similar to E.coli PMID: 16472375.  So
whatever we decide should be applied to all relevant cases.   When I talked to Herold he said that
it would be best to call the transcript tetracistronic  not polycistronic (the original name/def
was polycistronic).  I think the rRNA community tends to ignore the tRNAs and the tRNA community
returns the favor.

We may run into a problem fitting Drosophila into the current tree. Molecular biology of the gene
shows a 2s rRNA in the transcript.  FlyBase has the gene but no map data.


Karen responded and sent some thoughts on some other issues:

Date: Thu, 10 May 2007 14:46:41 -0700 (PDT)
From: Karen Christie <kchris@genome.stanford.edu>
To: Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>
Cc: Karen Christie <kchris@genome.stanford.edu>, harold Drabkin <hjd@informatics.jax.org>
Subject: Re: next meeting for rRNA processing?

Hi,

1. Regarding the tetracistronic txpt, I can go with that, but think we should at least add something
about the fact that tRNAs may also be present within the txpt, but that it is tetracistronic with respect
to the number of rRNA molecules produced. Alternately, we could call it 'multicistronic'.

2. Also, I did some poking around in AmiGO and it's clear to me that the 3 existing terms:
  35S primary transcript processing
  processing of 20S pre-rRNA
  processing of 27S pre-rRNA

have been used rather broadly.

I was thinking about what should be done with those terms and have some thoughts.

- Perhaps "35S primary transcript processing" could be merged up into
"rRNA processing", since it doesn't seem to me that there is real
distinction between this and "rRNA processing" itself.

The current def of "rRNA processing" is this:
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA
molecule.

which is basically exactly the same thing as processing of the "35S primary rRNA transcript"

I do think that the def should be changed so that it says "one or more mature rRNA molecules" rather than
just "a mature molecule".


- Perhaps these two terms could be renamed thusly:

  processing of 20S pre-rRNA -> maturation of SSU-rRNA (GO:0030490)

  processing of 27S pre-rRNA -> maturation of LSU-rRNA (GO:0030489)

3. I also added a bunch of terms to try to deal with the specifics that are known for rRNA processing in
yeast. No defs yet, thought I'd see what you two think first. The new terms are:
        exonucleolytic cleavages during rRNA processing
        maturation of 5.8S rRNA
        maturation of LSU-rRNA
        maturation of SSU-rRNA
and children.

I'm not sure whether we really need the first direct children of the three maturation terms. They do
serve to group the terms that are relevant to a given type of primary txpt and are parallel to the way
we've done the endonucleolytic cleavage terms, so maybe this is fine.

You can get the file from here again:

ftp://genome-ftp.stanford.edu/pub/people/curator/

Discussion: At the meeting, we discussed the 3 items from Karen's last email:

  1. Use of words "tricistronic", and "tetracistronic" for transcripts that contain tRNAs as well as rRNAs.
    • We agreed that this is OK as long as we add a clarification into the definition.
    • We opted for the def over the comment as the comment is frequently not seen.
  2. dealing with the 3 older terms
    • We all agreed that "35S processing" (GO:0006394) could be merged up into "rRNA processing"
    • We all agreed that "processing of 20S pre-rRNA" (GO:0030490) -> maturation of SSU-rRNA
    • Karen realized that "processing of 27S pre-rRNA" (GO:0030489) probably can't be renamed as "maturation of LSU-rRNA" because the 27S still also contains the 5.8S. She'll rethink the fate of this term
  3. Karen's maturation terms
    • We all agreed that this looked like a reasonable way to go.
    • We also agreed that the grouping terms under the maturation terms are good. They keep the various terms for a type of transcript together, and can also be used when all you know is that it effects the maturation of that rRNA species in some way, but you don't know the specific step.

To do List for next time:

  • Harold
    1. Check on processing of 5S rRNA (the one not from the rDNA repeat)
    2. maturation terms for bacterial rRNA
  • Karen
    1. finish defs for proposed maturation terms, etc.
    2. rethink fate of "27S rRNA processing" term
    3. check Archaeal
  • Ceri
    1. look up drosophila 2S rRNA?
    2. Maturation terms for tetracistronic rRNA

Karen will make today’s edits available on the ftp site for Harold and Ceri to work on. It is here:

ftp://genome-ftp.stanford.edu/pub/people/curator/gene_ontology_edit-rRNA_ideas20070518.obo

Harold and Ceri edit in their own copies and send them to Karen to merge into one file.

Next Meeting: May 25th at 10 am PST


May 25th, 2007 session

Present: Harold Drabkin, Karen Christie, Ceri Van Slyke

Discussion: At the meeting, we discussed:

  1. Harold's new term 'maturation of 5S rRNA'.
    • We realized that Ceri had also created a 'maturation of 5S rRNA' term.
    • Further examination indicated that Harold's term was specific for the 'generation of mature 3'-end of 5S rRNA from RNA polymerase III transcript' so it was thusly renamed and given parentage under Ceri's more general 'maturation of 5S rRNA' term.
  2. fate of the term 'rRNA 3'-end processing' (GO:0031125)
    • AmiGO only shows this being used for a couple S. pombe annotations, 1 IGI and 1 NAS. Harold looked at the reference for the IGI and felt that so far this has only been used for 3'-end processing of the LSU in pombe, so in our draft file, we merged this into this term:
      • generation of mature 3'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
    • Alternatively, we could obsolete this term and suggest consideration of all of the 'generation of mature 3'-end of ____ rRNA ...' terms
    • Midori, opinions?
  3. Ceri's new terms for processing of the primary rRNA transcript in Drosophila and other Dipteran flies.
    • The basic terms under the 'endocleolytic cleavages during rRNA processing' branch looked fine.
    • We also gave them additional parentage under the relevant maturation terms.
    • We also created 2 new maturation terms for 'maturation of 2S rRNA' and 'maturation of 4.5S rRNA'
  4. dealing with the old term "processing of 27S pre-rRNA" (GO:0030489)
    • Because the 27S rRNA still contains two pre-rRNAs, it will not correspond to any specific term in the new organization because we are making terms that relate to maturation of a specific final rRNA, not to any processing intermediates. Thus Karen proposed that we will need to obsolete this term and suggest 1 or more replacement terms.
    • Looking at AmiGO, almost all of the annotations to this term are from SGD. There are 2-3 S. pombe annotations that are ISS to SGD genes and 1 Drosophila annotation that was ISS from a couple UniProt IDs (one from mouse and one from Xenopus). With this knowledge and also that I'd want to reannotate all the SGD genes annotated to this term anyway, we're thinking that we can obsolete this term and suggest either of these two terms:
      1. maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) GO:0000466
      2. maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) GO:0000463.
    • Midori, opinions?

To do List for next time:

  • Harold
    1. maturation terms for bacterial rRNA
  • Karen
    1. finish defs for proposed maturation terms, etc.
    2. check Archaeal
  • Ceri
    1. a little bit more research into drosophila 2S rRNA


Karen will make today’s edits available on the ftp site for Harold and Ceri to work on. It is here:

ftp://genome-ftp.stanford.edu/pub/people/curator/gene_ontology_edit-rRNA-20070525.obo

Harold and Ceri can edit in their own copies and send them to Karen to merge into one file.

NOTE: Shortly after the meeting, Karen realized that there is already a term for 'RNA 3'-end processing' that has a number of child terms like 'mRNA 3'-end processing', 'snoRNA 3'-end processing', etc. Thus, I think it might be better to leave the existing 'rRNA 3'-end processing' term as it was. The specific 'generation of mature 3'-end of ___' terms can just get additional parentage under the 'rRNA 3'-end processing' term. A file with this alternative is here:

ftp://genome-ftp.stanford.edu/pub/people/curator/gene_ontology_edit-rRNA-20070525-alt.obo

Next meeting: June 1st at 10 am Pacific


June 1st, 2007 session

Present: Harold Drabkin, Karen Christie, Ceri Van Slyke

Discussion:

We discussed the child terms for the two new maturation terms Harold had put in for maturation of bacterial SSU and LSU rRNAs and changed some of the relationships so that an given step can be made a child of a 'maturation of LSU' or 'maturation of SSU' term, rather than all endonucleolytic cleavages of the bacterial pre-rRNA txpt automatically being children of both of these maturation terms. We also removed the specific reference to 'by RNase III' from these defs so that these terms will not be too narrow if other bacteria with the same txpt organization use something other than RNase III.

In response to last week's edits Midori had sent some comments by email, copied below, so we went through Midori's email and made the suggested corrections.

Date: Wed, 30 May 2007 14:42:42 +0100 (BST)
From: Midori Harris <midori@ebi.ac.uk>
To: Karen Christie <kchris@genome.stanford.edu>
Cc: Ceri Van Slyke <van_slyke@uoneuro.uoregon.edu>, Harold Drabkin <hjd@informatics.jax.org>
Subject: Re: rRNA processing stuff

Hi,

This has realy come a long way -- I'm impressed. Thanks for all the work you're putting in!

I like the latest idea (below and in RNA-alt.obo) for dealing with rRNA 3'-end processing

The proposal to obsolete GO:0030489 sounds reasonable. I recommend sending the usual "Alert" email with the
two-week notice period, so we can honestly say we're following procedure.

A few more small things:

Merging '35S primary transcript processing' (GO:0006365; typo on wiki) into rRNA processing looks good, although
I wonder if the synonym scope for the "35S processing" string should be  narrow -- are there any primary
transcripts of different sedimentation coefficient? (If not, the synonym can stay exact.)

I presume the defs will be filled in for GO:000459, 461, 462 and 464-469 -- Karen's to-do #1?

Missing 'S' in GO:0000460 def.

It might be worth saying what 'ETS' stands for in the GO:0000446 def.

I'll try to make a brief appearance at the Friday chat, but since it starts at 6pm UK time I probably won't stay
for the whole thing (also - the invite I got says 10 PM, not am). It will be great to have this go live.

cheers,
midori

To do List for next time:

  • Karen
    1. def for GO:0000469 (missed this one last week)
    2. check where "cleavage at C2" synonym belongs (currently on 2 terms)
    3. check Archaeal
  • Everyone check over the whole file for
    1. general logic
    2. defs, correctness, typos, etc.
    3. residual comments, make sure we don't still have any comments to ourselves which should not become public

Karen will make today’s edits available on the ftp site for Harold, Ceri, and MIdori to look at on. It is here:

ftp://genome-ftp.stanford.edu/pub/people/curator/gene_ontology_edit-rRNA-20070601.obo

Summary

We think we are just about done with this. So we have not scheduled another meeting. Instead, all 3 of us, and MIdori if interested, will go through all the terms, defs, comments, synonyms, etc. to see if we've missed anything. The deadline for comments is June 7th. If we find anything that prevents proceding, we plan to send out an email about the proposed obsoletion of GO:0030489 (27S rRNA processing) on June 11th and can then make the changes on June 25, assuming no one objects to the obsoletion.