This page is part of the Biotwiki collaboration platform. For more information about Biotwiki see Main. If you want to get started with Biotwiki please have a look at BioTwikiHelp. Once you have registered you can edit this page and actively contribute to the discussion.

Introduction

This website offers you the oportunity to contribute to a discussion concerning the whole exercise of renaming checkpoint genes. Below you will find the original letter that initiated this discussion:

Original Letter

---

Dear Checkpoint Person(!)

Science Magazine has approached us and suggested that the checkpoint field try to simplify the nomenclature used for checkpoint proteins. The confusing nomenclature between different organisms has been a persistent irritation for people who wish to understand the field, and even causes significant problems for those working close to the field. It is our belief that the time is right to develop a unified nomenclature for checkpoint genes/proteins, based on their known functions and associations. Below is a list of those genes/proteins that we propose should be renamed.

We feel it would be beneficial to consult the community on this important issue, and thus we invite labs and individuals to enter a "competition" to suggest names. We will then collate suggestions and present a selection of options for a web-based vote by the community. To encourage participation, we are offering a small prize to the people suggesting the names finally chosen.

As an initial suggestion, we feel that the use of the human nomenclature should be adopted for the central proteins whose common functions are relatively clear. The reason that we favour the human nomenclature is four-fold.

1st, The checkpoint and DNA damage signalling field in humans will probably show the largest growth in the future.

2nd, It would be very difficult for the human checkpoint community to agree on renaming genes. This is especially true for genes associated with human diseases such as ATM or NBS1.

3rd, Using the human gene, or a similar 3 letter designation, as a name directly underscores the significance of the work in model organisms to human health.

4th, Using the human gene names might enhance funding opportunities in the future for work on similar genes in model organisms.

While an argument can be made that giving genes the same names might inappropriately suggest they have the same function, this argument would carry forward to all genes, suggesting that no two genes in different species be given the same name because they might not have identical functions. In fact, the majority of functions are conserved among checkpoint genes and the differences often have to do with the biology of the organism and downstream effectors as opposed to any real differences in the functions of the genes themselves. So, while this argument has some merit, we feel the strengths of common names overcomes the potential oversimplification.

Therefore we would like to propose the following human names to be used for their yeast, fly and other eukaryotic counterparts:

ATM for Tel1 ATR for Mec1, rad3 and mei-41 ATRIP for Ddc2/Lcd1/Pie1, rad26 and mus304. The ATRIP name will have to be abbreviated to three letters, such as ATI1 or ATR2

Chk1 for all the Chk1 Chk2 for Rad53 and cds1

The largest problem has to do with the human Rad17, and the PCNA-related complex of Rad1, Rad9 and Hus1 complex commonly referred to as the 911 complex. As the RAD nomenclature is difficult to remember, not to mention the fact that we use the same name to mean different checkpoint proteins in different species, it is the most in need of new names as the human genes suffer from the same problem as the yeast genes.

Other genes, such as the BRCT-repeat proteins may also need to be renamed. However we do not feel that sufficient knowledge is currently available to determine which are homologues. Thus these proteins may need to await further analysis before a path is clear for renaming them. We will entertain names for future selection, so send in your ideas. After names are assembled, a second email will be sent with a few of the finalist names and we can go from there. To ease the transition in the literature, after we have agreed upon a name, we urge everyone to use both names in abstracts for several years to cement the connections and to aid in Medline searching, etc.

To participate please e-mail a uniform nomenclature suggestion in this format to univ@bcmNOSPAM.tmc.edu and put "Nomenclature" and your "Lab Name" in the subject line to allow us to identify the email.

Suggestions for naming genes.

1. Try to avoid names already given to other existing genes in yeast or other organisms.

2. A name that gives a clue to the function is often a good choice. Remember, people from disparate fields will be using these names to remind them of their roles.

3. Having a name that is easy to say is often useful. This may mean having a vowel in it. 4. A name whose three letter acronym is already common in a different context makes it easier to remember and may stick more easily, i.e. ATM, NBC, CBS etc.

Be creative! It often helps to write out the alphabet and put words for each letter that refer in some way to the proteins or pathways in question. These become a source for generating the various acronyms.

Sincerely,

Ted Weinert

Tony Carr

Steve Elledge

---

Reactions

This letter led to several reactions from the checkpoint community, click on the links below if you want to read them. Please note that due to formatting problems, these letters do not contain the suggested nomenclatures in a table format.

• HartwellLetter
• NurseLetter
• KastanLetter
• HawleyLetter
• DaveyLetter
• HaberLetter
• KolodnerLetter
• LehmannLetter
• RussellLetter
• LydallLetter
• YanagidaLetter
• CampbellLetter
• SugimotoLetter
• ToczyskiLetter
• KarnitzLetter
• PlonLetter
• RothsteinLetter

Suggestions made in the above letters have been summarised in the table below:

Current names			Proposed unifying names
Mammalian	Budding Yeast	Fission Yeast	Elledge	Karnitz	Sugimoto	Campbell	Lydall	Russell	Lehmann	Haber	Davey	Toczyski
Atm	Tel1	Tel1	Atm				Chk4
Atr	Mec1	Rad3	Atr				Chk3
Atrip	Ddc2/Lcd1/Pie1	Rad26					Chk5				Atl1/Atr2	Atr2
Chk1	Chk1	Chk1	Chk1				Chk1
Chk2	Rad53	Cds1	Chk2				Chk2
Rad17	Rad24	Rad17	Nel1	Chk3/Cll1	Lpc1	Clu6	Chk10	Chl17	Crf1	Rfc6/Ccl1	Chk17
Rad1	Rad17	Rad1	Nec1	Chk4/Clm1	Pcc1	Pcn2	Chk11	Chs8	Cpc1/Chp1	Cpc1	Rad1
Rad9	Ddc1	Rad9	Nec2	Chk5/ Clm2	Pcc2	Pcn3	Chk12	Chs9	Cpc2/Chp2	Cpc2	Chk9
Hus1	Mec3	Hus1	Nec3	Chk6/Clm2	Pcc3	Pcn4	Chk13	Chs10	Cpc3/Chp3	Cpc3	Hus1
Claspin	Mrc1	Mrc1					Chk 21
BRCA1	Rad9	Rhp9/Crb2					Chk 20
Top BP1	Ddc11	Cut5					Chk22

Discussion

Feel free to comment on this issue in the box below. To add your comments and edit this page you need to be registered with the Biotwiki collaboration platform. For more information about Biotwiki and registration see Main. If you want to get started with Biotwiki please have a look at BioTwikiHelp.

---

---

>.<