Difference between revisions of "RNA processing"

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(March 26, 2007 session)
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'''To Do list''':
 
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#*mitochondrial in fungi
 
#*mitochondrial in fungi
 
#*in archaea
 
#*in archaea
#Harold: nuclear in mammals
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== April 2nd, 2007 session ==
 
== April 2nd, 2007 session ==

Revision as of 12:51, 7 May 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

Monday April 2, 2007 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 defs:

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

April 17, 2007 session

Monday April 17, 2007 present: Harold Drabkin, Ceri Van Slyke