ntr: CRISPR element metabolism

[gocentral]

Hello,

I am submitting this request on behalf of teammate Dan Haft.

Dan and colleagues have recently published a paper describing a set of protein families associated with a DNA repeat called CRISPR. It seems that many of these proteins are involved in the maintenance or expansion of the CRISPR element itself. Therefore, Dan would like a term to describe this process.

name: CRISPR element metabolism parent: GO:0006259 "DNA metabolism" relationship to parent: isa def: Any process involved in the maintenance of CRISPR repeat clusters, capture of new spacer elements, expansion or contraction of clusters, propagation of the leader sequence and repeat clusters within a genome, transfer of repeat clusters and CRISPR-associated (cas) genes to new genomes, transcription of the CRISPR repeat arrays into RNA and processing, and interaction of CRISPR/cas loci with the host genome. CRISPR (clustered regularly interspaced short palindromic repeat) elements are a family of sequence elements containing multiple direct repeats of 24-48 bp with weak dyad symmetry which are separated by regularly sized nonrepetitive spacer sequences. def ref: from PMID:16292354

Thanks, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/3040":https://sourceforge.net/p/geneontology/ontology-requests/3040

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Hmmm - we also have a term 'rDNA maintenance ; GO:0043007' (The maintenance of fidelity and copy number of rDNA repeats.) which seems like it should be grouped with this term. How about we make a new parent term 'maintenance of DNA repeat elements' as a child of both 'chromosome organization and biogenesis ; GO:0051276' (or possibly 'chromosome organization and biogenesis (sensu Eukaryota)' - do prokaryotes have repeat elements?) and 'DNA metabolism ; GO:0006259'. This term and 'rDNA maintenance' can be its children...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=482944

Hi Jane,

It can't be a child of the sensu Eukarya term since indeed proks do have repeats. The CRISPRs are found in proks and it is for proks that I requested the term.

Your plan sounds good to me.

Thanks, Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=451873

Oops - good job I checked! Okay - added:

maintenance of DNA repeat elements ; GO:0043570 as a child of 'chromosome organization and biogenesis ; GO:0051276' and 'DNA metabolism ; GO:0006259'

with child: maintenance of CRISPR repeat elements ; GO:0043571

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242