Difference between revisions of "McClean: Yeast Nomenclature"

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==Overview==
 
==Overview==
  
'S. cerevisiae' researchers have a systematic approach for describing genotypes of yeast strains.  You need to follow this system when writing papers, protocols, and when entering yeast strains into the lab database.   
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''S. cerevisiae'' researchers have a systematic approach for describing genotypes of yeast strains.  We need to follow this system when writing papers, protocols, and when entering yeast strains into the lab database.   
  
Much of this information is taken from the "Methods in Yeast Genetics" book from Cold Spring Harbor LaboratorySee the references below.
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Yeast nomenclature is covered well in the articles listed in the references, so I won't recapitulate all of the details here.  You should refer to these references when you have questionsI will just list some of the common conventions that you might need when entering strains into the lab database.
  
 
==Nomenclature==
 
==Nomenclature==
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===Genetic Background===
 
===Genetic Background===
  
 
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===Alleles===
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====Alleles created by recombinant DNA technology====
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# '''Disruptions'''
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# '''Deletions'''
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#* Deletions are written as the name of the gene that is altered following by -Δ; for example arg2-Δ1, where the number 1 denotes a specific complete or partial deletion of arg2.
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#'''Replacements'''
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#* Replacements should be written as the name of the gene that is replaced followed by the symbole Δ::.  Examples:
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#** If you deleted the entire open reading frame of the GAL1 gene with a drug resistance cassette (such as NatMX for ClonNat resistance) you would write gal1Δ::NatMX. 
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#**If you deleted the GAl1 open reading frame with a fluorescent reporter (for instance, with GFP-KanMX if you wanted a quick reporter of P<sub>GAL1</sub> promoter activity) you would write the genotype as ga1Δ::GFP-KanMX
  
 
==Notes==
 
==Notes==
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Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.
 
Please sign your name to your note by adding <font face="courier"><nowiki>'''*~~~~''':</nowiki></font> to the beginning of your tip.
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'''*[[User:Megan N McClean|Megan N McClean]] 11:29, 16 November 2012 (EST)''':I got some helpful tips from P. Gibney on how he writes out promoter replacements:
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* YFG(-1 to -n)Δ::KanMX-GAL1(-1 to -n)
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* YFGprΔ::KanMX-GAL1pr
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So far as we could figure out there is no perfect/official way to do it, but this notation gives you a clear idea of what was done.  Especially the detailed YFG(-1 to -n) notation which tells you which part of the promoter was actually replaced with which part of the GAL1 promoter.
  
 
==References==
 
==References==
 
Burke, D. Dawson, D. & Sterns, T.  2000 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual ''Cold Spring Harbor Laboratory Press''
 
Burke, D. Dawson, D. & Sterns, T.  2000 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual ''Cold Spring Harbor Laboratory Press''
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Sherman, F. 2002 Getting started with yeast ''Methods Enzymol'', 350, 3-41
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[http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf ''Saccharomyces cerevisiae'' Genetic Nomenclature Guide]
  
 
==Contact==
 
==Contact==
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Nomenclature
 
Naming Yeast Strains
 
Now that you've become (somewhat) comfortable working with yeast in the lab,
 
it's time to master some of the jargon associated with yeast…
 
S. cerevisiae researchers have adopted a systematic approach for describing the
 
genotypes of their yeast strains. Genes that have been studied or characterized in some
 
way often have a "common" name ascribed to them, and this name generally consists of
 
three letters and a number. For example, LEU2 refers to a gene encoding an enzyme in
 
the leucine biosynthetic pathway, and PDR3 refers to a gene encoding a transcription
 
factor involved in pleiotropic drug resistance. The table below describes the basics of
 
yeast genetic nomenclature which is always typed up in italics.
 
Wild-type alleles are written in all caps LEU2
 
And sometimes with a "plus" sign LEU2+
 
Recessive mutant alleles are written in lower case arg2
 
And may include an allele number arg2-9
 
Dominant mutant alleles are written in all caps
 
And should include an allele number PDR3-11
 
Or other notation to indicate it is not wild-type. OLIr
 
Besides its "common" name, each gene has a systematic name that refers to its
 
precise position in the genome…
 
YNL323w
 
This is a yeast gene
 
On chromosome XIV (N is the 14th letter in the alphabet)
 
This gene is on the left arm of the chromosome
 
It is the 323rd gene away from the centromere
 
It is on the "Watson" strand
 
I
 

Latest revision as of 08:30, 16 November 2012


Overview

S. cerevisiae researchers have a systematic approach for describing genotypes of yeast strains. We need to follow this system when writing papers, protocols, and when entering yeast strains into the lab database.

Yeast nomenclature is covered well in the articles listed in the references, so I won't recapitulate all of the details here. You should refer to these references when you have questions. I will just list some of the common conventions that you might need when entering strains into the lab database.

Nomenclature

Chromosomal Genes

Nonmendelian Determinants

Genetic Background

Alleles

Alleles created by recombinant DNA technology

  1. Disruptions
  2. Deletions
    • Deletions are written as the name of the gene that is altered following by -Δ; for example arg2-Δ1, where the number 1 denotes a specific complete or partial deletion of arg2.
  3. Replacements
    • Replacements should be written as the name of the gene that is replaced followed by the symbole Δ::. Examples:
      • If you deleted the entire open reading frame of the GAL1 gene with a drug resistance cassette (such as NatMX for ClonNat resistance) you would write gal1Δ::NatMX.
      • If you deleted the GAl1 open reading frame with a fluorescent reporter (for instance, with GFP-KanMX if you wanted a quick reporter of PGAL1 promoter activity) you would write the genotype as ga1Δ::GFP-KanMX

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

  1. List troubleshooting tips here.
  2. You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
  3. Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.

*Megan N McClean 11:29, 16 November 2012 (EST):I got some helpful tips from P. Gibney on how he writes out promoter replacements:

  • YFG(-1 to -n)Δ::KanMX-GAL1(-1 to -n)
  • YFGprΔ::KanMX-GAL1pr

So far as we could figure out there is no perfect/official way to do it, but this notation gives you a clear idea of what was done. Especially the detailed YFG(-1 to -n) notation which tells you which part of the promoter was actually replaced with which part of the GAL1 promoter.

References

Burke, D. Dawson, D. & Sterns, T. 2000 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual Cold Spring Harbor Laboratory Press

Sherman, F. 2002 Getting started with yeast Methods Enzymol, 350, 3-41

Saccharomyces cerevisiae Genetic Nomenclature Guide

Contact

or instead, discuss this protocol.