Cell Cycle

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The representation of the cell cycle in GO is split into two sections: the physical processes that occur and the temporal stages—prophase, anaphase and so on—used to describe sets of events. This method of representation is used to prevent true path problems when organisms differ from the "canonical" (usually S. cerevisiae) cell cycle.

Terms and Structure

The cell cycle node sits under cellular process ; GO:0007049 and is split into types of cell cycle (meiotic or mitotic) and stages (M phase, S phase, etc.), plus a regulation term.

   cell cycle
       [p] interphase
           [i] interphase of meiotic cell cycle
           [i] interphase of mitotic cell cycle
           p] S phase
           [p] G1 phase
           [p] G2 phase
       [p] M phase
       [i] meiotic cell cycle
       [i] mitotic cell cycle
       [p] regulation of cell cycle

Taking the example of M phase of the mitotic cell cycle, this is the structure of the child terms of M phase. Note that the terms representing temporal phases are not linked to those representing physical events.

   M phase of mitotic cell cycle
       [p] mitotic anaphase
       [p] mitotic metaphase
       [p] mitotic prometaphase
       [p] mitotic prophase
       [p] mitotic sister chromatid segregation
       [p] mitotic telophase
       [p] regulation of mitosis

The physical events associated with mitotis and meiosis are mainly found under the term chromosome segregation, defined as "the process in which genetic material, in the form of chromosomes [or chromatids], is organized and then physically separated and apportioned to two or more sets". The related term chromosome separation refers to the detachment of chromosomes from each other as they move towards the spindle pole.

   mitotic sister chromatid segregation
       [p] attachment of spindle microtubules to kinetochore during mitosis
       [p] attachment of spindle microtubules to mitotic chromosome
       [p] mitotic chromosome condensation
       [p] mitotic chromosome decondensation
       [p] mitotic chromosome movement towards spindle pole
       [p] mitotic metaphase plate congression
       [p] mitotic sister chromatid cohesion
       [p] mitotic sister chromatid separation

Standard Definitions

  • any cell cycle phase (e.g. M phase, telophase): Progression through [phase name], [description of phase].
  • any cell cycle process (e.g. mitotic chromosome condensation): The cell cycle process whereby [description of process].

Cytokinesis

Cytokinesis is placed under cell division but not under cell cycle, something which seems counterintuitive to many. This is because bacteria, which do not have a cell cycle, undergo cytokinesis. Organisms that do have a cell cycle can use more specific terms, such as cytokinesis after meiosis I and cytokinesis after mitosis to represent cytokinesis in their organism.

NOTE JULY 2018 PG: Cytokinesis is a cell cycle process


Working group Summary

The cell cycle terms in GO haven't been touched for a while. There's a number of problems with the current arrangement since the cell cycle is largely based on timing. Along with cell cycle experts, we need to find a better way to model the cell cycle in GO.

NOTE: this is an old page, created to kick off the project and the Content Meeting in Hinxton.


Personnel

GO

  • Val
  • GOEds (Jane, Paola, David, Tanya)
  • Rachael Huntley (UniProt-GOA)
  • Mary Dolan (MGI)

Reactome

  • Bijay Jassal
  • Lisa Matthews

External experts

  • Jacqueline Hayles
  • Takashi Toda
  • Rob De Bruin

Key Issues

Summary from Val:

I had a read through most of the SF items and this is a general flavour of the problems. Problems include:

  1. General inconsistencies: [1] identifies some inconsistencies under cell cycle, and raises the questions
  2. Where does the cell cycle begin and end what do we mean by cell cycle as a process?
  3. Should we separate "cell cycle events " like DNA replication, chromosome segregation, from the cell cycle control system[2]
  4. Problems linking events to timing, because events occur in different phases in different organisms [3]
  5. Should we have phases (S-phase, M-phase, G1 phase which are currently in the process ontology), OR should we only have regulation of cell cycle phase transitions?
  6. A lot of issues arise because we don't have a clear idea where sub processes begin and end. So for instance is spindle elongation part of chromosome segregation? [4] e.g. Chromosome segregation occurs in two phases: chromosomes move towards spindle poles during anaphase A, and spindle poles separate from each other during anaphase B.(PMID: 11309422). But the definition of chromosome segregation in GO ends when the chromosomes reach the spindle poles, suggesting that spindle elongation comes after:

Viruses and the host cell cycle

Currently two separate cell cycle grouping terms in the viral node. Should they be merged or related? (once sorted out what processes are part of the cell cycle, and what processes regulate the cell cycle):

  • modification by virus of host cell cycle regulation ; GO:0019055
  • modulation by virus of host cell cycle ; GO:0060153


SF items

Resources

Cell Cycle Ontology


Papers

Meetings

Cell Cycle Content Meeting (EBI, Hinxton, UK)

Feb. 28th and March 1st 2013.

Link to meeting page: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013

Cell Cycle Content Meeting follow-up 27 March 2013

Agenda


Cell Cycle Content Meeting follow-3 (date TBD)

Agenda

Cell Cycle Content Meeting follow-up 12 April 2013

Discussion after GOC Consortium meeting, Churchill College, Cambridge

Minutes



Back to: Notes on specific terms