RNA processing

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Revision as of 13:41, 7 May 2007 by Kchris (talk | contribs) (Work from April 9th, 2007 session)

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Initial session on March 26, 2007

Monday March 26, 2007 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

Work from 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???

Work from April 9th, 2007 session

Monday April 9, 2007 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