Subject: Re: FB Help Mailer: 041 gene name Date: 27 August 2009 09:42:12 BST Hi Mike, Yes, the inconsistency in the Lilly et al 1994 paper is certainly strange. However, in terms of FlyBase curation, we don't capture gene names when they are used generically to refer to the gene family, as is the case in the Abstract and Introduction of the Lilly et al 1994 paper. (And we don't capture anything at all from the Introduction of any paper.) That's why we would only capture the gene name 'Drosophila myocyte-specific enhancer factor 2' from this paper, as it's the only Drosophila-specific fullname that's mentioned. (And, as I said previously, we'd convert that fullname to 'Myocyte-specific enhancer factor 2' as the official FlyBase name to conform to our nomenclature rules.) We don't normally action gene renames based on reviews, but it's clear from those you cite that 'myocyte enhancer factor 2' is the preferred fullname. Your point that Mef2 is not specifically expressed in myocytes is important - we do change FlyBase gene symbols/names where the current nomenclature is shown to be inaccurate or misleading. Same comment as above wrt the Lilly et al (1995) paper - the name 'myocyte enhancer-binding factor 2' in the abstract is used generically to refer to the family of genes across all organisms, so we wouldn't capture that as a fullname (synonym) for the D. melanogaster gene. Your assertion that the mammalian gene is now always referred to as "Myocyte enhancer factor 2"is supported by a quick look at the HGNC website. Given your comments here, it's now clear to me that 'myocyte enhancer factor 2' is the preferred, more accurate and most pragmatic fullname for this gene. So, I am happy to change the name to 'Myocyte enhancer factor 2' in FlyBase. I don't think there's a need to contact the Olson and Cripps labs about this - it's clear from their publications that they agree with you. Thanks again for alerting us to the problems with this gene name. Best, Steven. ------------------------------- Subject: Re: FB Help Mailer: 041 gene name Date: 26 August 2009 23:18:50 BST Dear Steven, I take your point about the Lilly et al 1994 paper in PNAS from the Eric Olson lab. However, even before the first para of the Results in this paper, they already twice refer to it as "Myocyte enhancer factor 2", in both the Abstract and the Introduction. So, the first Drosophila mef2 paper is not itself consistent. This being the case one could designate the gene name as "myocyte enhancer factor 2" and still cite Lilly et al (1994). The original and still the main player in the Mef2 field is the Olson lab. As I said previously, Mef2 was first described in mammalian cells where they originally called it "myocyte-specific enhancer-binding factor 2". This name is undoubtedly a bit cumbersome and so it is understandable why it has been superseded by the more succinct (and more accurate) "Myocyte enhancer factor 2" in their authoritative reviews of the field covering both mammalian and Drosophila research (Olson et al (1995) Dev Biol 172, 2-14; Black and Olson (1998) Ann Rev Cell Dev Biol 14, 167-196; and Potthoff and Olson (2007) Development 134, 4131-40) and in their many other papers too. It is more accurate because a body of work has shown that Mef2 is not specifically expressed in myoctyes. This being the case the name "myocyte-specific enhancer factor 2" is actually a bit misleading. As you say, the Olson lab do refer to Mef2 in their first paper (Lilly et al (1994)) once as"myocyte-specific enhancer factor 2". Equally, in the first functional paper on Drosophila Mef2 also from their lab (Lilly et al (1995)) they refer to it as "myocyte enhancer-binding factor 2". So, one can see that the contraction of the original very long mammalian designation was not always done in the same way in the early Drosophila papers. As far as I am aware the mammalian gene is now always referred to as"Myocyte enhancer factor 2". While all in favour of canvassing opinion, it might be difficult to get everyone's views. This being the case I think it would be reasonable to go for the most commonly used, the most accurate, and the most succinct name, ie. "myocyte enhancer factor 2", especially as that is the one used by the Eric Olson lab. It is also that used by the Richard Cripps lab, who have published perhaps most on Drosophila mef2. You could ask one or both of these labs for their view if you felt this was a good idea. All the best, Mike. ------------------------------- Hi Mike, I haven't been able to confirm it, but it looks like Mef2 got the name of 'Myocyte enhancing factor 2' in FlyBase as a result of an internal processing error. Two papers (FBrf0201668 == Gabut et al., 2007 & FBrf0190812 == Cho et al., 2005) used this name, and this somehow became the 'official' name in FlyBase when the data from these papers entered the database. Apologies for that. Regarding how we name genes in FlyBase, we usually use the first meaningful symbol (abbreviation) and fullname published in a peer-reviewed paper. See our nomenclature doc for more details: http://flybase.org/static_pages/docs/nomenclature/nomenclature3.html#1.2. I've done a bit of research on the Mef2 nomenclature myself, and largely agree with the points in your original email. The first published paper mentioning the D. melanogaster gene appears to be: FBrf0073742 == Lilly et al., 1994. Here, the authors are very explicit about their preferred symbol and fullname. They state in the first paragraph of the results: "Thus, we designated the protein encoded by this cDNA D-MEF2, for Drosophila myocyte-specific enhancer factor 2, and we designated the gene encoding this protein D-mef2." You can read in our nomenclature doc that we always drop the 'D' (for 'Drosophila') prefix when naming genes in FlyBase, and we also make the first letter uppercase when the gene is "named for some aspect of the wild-type molecular function or activity." So, the FlyBase nomenclature ought to be: Symbol: Mef2 Name: Myocyte-specific enhancer factor 2 I realise that this isn't your preferred name of 'myocyte enhancer factor 2'. If this is clearly the preferred fullname in the community, then we can change the fullname to this variant. It's not clear to me from our records whether this is the case or not. If you're so-minded, you could canvas opinion from all interested parties on this matter and then send a mail to FlyBase showing there's a consensus to change to 'Myocyte enhancer factor 2'. Hope this helps, Steven. -- Steven Marygold FlyBase ------------------------------- Dear FlyBase, I note that in FlyBase the gene with the symbol Mef2 gene is named Myocyte enhancing factor 2. However, the original widely used name was myocyte enhancer factor 2, or similar (see below). Moreover, "enhancer" (as in a DNA regulatory element) has a somewhat different sense to "enhancing". As far as I am aware the first paper describing Mef2 was in mammalian cell culture and the full name given was myocyte-specific enhancer-binding factor 2. The reference is: Gossett LA, Kelvin DJ, Sternberg EA, Olson EN. Mol Cell Biol. 1989 Nov;9(11):5022-33. A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes. The first three papers on Drosophila Mef2 refer to it as myocyte enhancer factor (MEF) 2, myocyte-specific enhancer factor 2 (MEF2), and myocyte enhancer-binding factor 2 respectively. The references are: Lilly, B., Galewsky, S., Firulli, A.B., Schulz, R.A., Olson, E.N. (1994). D-MEF2: A MADS box transcription factor expressed in differentiating mesoderm and muscle cell lineages during Drosophila embryogenesis. Proc. Natl. Acad. Sci. U.S.A. 91(12): 5662--5666. Nguyen, H.T., Bodmer, R., Abmayr, S.M., McDermott, J.C., Spoerel, N. (1994). D-mef2: A Drosophila mesoderm-specific MADS box-containing gene with a biphasic expression profile during embryogenesis. Proc. Natl. Acad. Sci. U.S.A. 91(16): 7520--7524. Taylor, M.V., Beatty, K.E., Hunter, H.K., Baylies, M.K. (1995). Drosophila MEF2 is regulated by twist and is expressed in both the primordia and differentiated cells of the embryonic somatic, visceral and heart musculature. Mech. Dev. 50(1): 29--41. The first three papers analysing Drosophila mef2 function all published in 1995 also refer to the gene similarly. They are; Science. 267(5198):688-93. Genes Dev. 9(6):730-41. Dev Biol. 171(1):169-81. Perhaps the most prominent review on Mef2 that followed all the initial work in both mammals and Drosophila also refers to Mef2 as myocyte enhancer factor-2. The reference is: Transcriptional control of muscle development by myocyte enhancer factor-2 (MEF2) proteins. Black BL, Olson EN. Annu Rev Cell Dev Biol. 1998; 14:167-96 . I don't know how FlyBase decides on the gene name, but in the light of the above I am curious to know how the designation "Myocyte enhancing factor 2" occurred. If it is possible and within your operating rules, I think you should consider modifying the name to myocyte enhancer factor 2. I cannot be sure, but think that in an earlier version of FlyBase the gene may well have been called myocyte enhancer factor 2, or similar. At least I haven't noticed this previously.. I hope this is helpful. Yours sincerely, Michael Taylor.
