Subject: Re: FlyBase Query (cy1670)
..
..(Hochman changed) the nomenclature of the alleles named in his first
paper with Gloor and Green (1964) in a subsequent paper, which he
authored alone (1971). We have carefully read all the literature
available, including short communications in DIS, have actually tested
all the alleles still available from FlyBase, and tried to give this
information in the paper (text and legend to Fig. 3). However, it
might still not be sufficiently clear, for which i apologize. I will
ask Erich Frei, who did most of this work together with Michael Daube,
to help you.
With best regards,
Markus
Dr. Markus Noll
Institute for Molecular Biology
University of Zürich
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
>Dear Dr Noll,
>
>I am currently curating your paper for FlyBase:
>
>Kronhamn et al., 2002, Development 129(4): 1015--1026
>
>I have some questions, as I have to admit, I am somewhat confused about
>the relationship between the genes you mention in the toy region, and
>the genes FlyBase has with similar names or synonyms.
>
>You describe an allele l(4)8 whose headless phenotype you discuss. You
>then state that it is allelic to toy. You cite the Hochman 1964 paper,
>for l(4)8, and I can find in that paper a complementation group that
>contains mutations 8 10 and 19 (Fig1).
>
>We have l(4)8 as a synonym for l(4)102CDg (specifically l(4)102CDg1)
>We have l(4)10 as a synonym for l(4)102CDh AND l(4)102CDg
>(l(4)102CDg2 aka l(4)8a)
>We have l(4)19 as a synonym for l(4)102EFf and l(4)102CDg
>(l(4)102CDg3 aka l(4)8b)
>
>This would suggest that the mutations 8 10 and 19 and thus the l(4)8
>'hdl' are alleles of l(4)102CDg, however you name (4)102CDg as a
>separate gene in Fig3. Which means that the gene FlyBase currently
>calls l(4)102CDg is probably not the gene you call l(4)102CDg.
>
>You mention that there has been confusion about nomenclature in this
>region, and I have had a look at the Hochman papers involved, but it
>hasn't really cleared things up for me.
>
>Is the toy allele 'l(4)8=hdl' allelic to any of the FlyBase genes?
>l(4)102CDh, or l(4)102CDg? Or is the allele l(4)8 you used not
>described in FlyBase (possibly merged with another l(4)102CDg by
>accident? when the symbol l(4)8 was reused)
>
>You mention that the allele you call l(4)102CDg3 was previously called
>l(4)19, which means that FlyBase probably assumed that it was the same
>as l(4)102CDg3 above. In which paper was this allele called l(4)19?
>
>Have we merged two genes by accident? l(4)102CDg with three alleles
>called 8 10 and 19 in the Hochman 64 paper A different gene with the
>single allele called by you 102CDg3?
>
>To summarise:
>
>You mention these three genes,
>102CDh (2 alleles)
>102CDg (1 allele)
>toy(l(4)8)
>
>FlyBase has currently,
>l(4)102CDh (3 alleles)
>l(4)102CDg (3 alleles)
>
>Can you help me establish which genes are which? Any new information
>you give us will be curated as a personal communication, if thats OK
>with you.
>
>Thanks
>
>Chihiro
>
>----------------------------------------------------------------------
>Chihiro Yamada.
>
>FlyBase (Cambridge)
>----------------------------------------------------------------------
Dear Chihiro,
..
Erich and I went once again through our notes and summarized our
findings and conclusions in the attachment that should answer all of
your questions and help you eliminate ambiguities in the annotations of
FlyBase.
With best regards, also from Erich,
Markus
\--
Here is what caused the confusion. In 1964, Hochman, Gloor, and Green
published a paper (Genetica 35, 109-126) describing 54 lethal mutations on the
4th chromosome, 36 of which were induced by X-ray by Gloor and Green, while
the remaining 18 were isolated as spontaneous mutations by Hochman, largely
from natural populations. These 54 mutations were grouped into
complementation groups, including one or several alleles. The X-ray induced
mutations were given numbers, while the spontaneous mutations were designated
by a two or three-letter code followed by a number. The X-ray induced and
spontaneous mutations were grouped into complementation groups. For example,
the following X-ray induced mutations were found in the same complementation
groups:
1, 27, 28, 32
2, 21, 23, 29, 34, 37, 38
4, 18, 20
5
6, 15, 36
7
8, 10, 19
11, 12, 24
13
and so on!
The confusion started when Hochman published the next paper in 1971 (Genetics
67, 235-252), in which he decided to 'replace the nomenclature used earlier
with one in which all lethals are symbolized by an italicized number, e.g.,
l(4)1, and all alleles found subsequently are given the same number and a
letter superscript. Thus the lethals allelic to 1 described earlier (27, 28,
and 32) become 1a, 1b, and 1c, respectively. This practice serves to release
integers such as 27, 28, and 32 in naming newly detected loci and it also
provides a means of computing rapidly the number of allelic mutations that
have occurred at each locus.'
In other words, the complementation groups above became:
l(4)1, l(4)1a, l(4)1b, l(4)1c
l(4)2, l(4)2a, l(4)2b, l(4)2c, l(4)2d, l(4)2e, l(4)2f
and so on.
Specifically, the alleles of the earlier complementation group, 8, 10, and 19,
were renamed as l(4)8, l(4)8a, and l(4)8b. As a consequence, 10 and 19
were 'released' and reused to designate new alleles of different loci!
Therefore, what later appeared as l(4)19 is not allelic to l(4)8, as the
uninformed reader might suspect, but rather represents a new locus!
In contrast, the mutant allele l(4)8 that Åsa Rasmuson-Lestander discovered
among the Umeå stocks to have a headless phenotype (Kronhamn et al.,
Development 129, 1015-1026, 2002) never changed its original name and was
still listed under this name in the Umeå stock list. We have shown that this
mutation is a deficiency of the toy gene that deletes the entire coding region
of the four last exons, exons 6-9. Because of its headless phenotype, we
named the l(4)8 allele toyhdl.
Apparently, FlyBase was also confused by the different nomenclatures of
Hochman. Therefore, all lethals on the 4th chromosome were given new names
according to their suspected cytological position. For example, l(4)8 was
also called l(4)102CDg1, while l(4)10 was called l(4)102CDh as well as
l(4)102CDg2 (aka l(4)8a). The trouble is that there are two different
l(4)10 mutations: one is the old mutation described in 1964, which in 1971 was
renamed l(4)8a by Hochman and later l(4)102CDg2 by FlyBase; the other
l(4)10 mutation was first published in 1971 and, accordingly, is not allelic
to l(4)8. This mutation was given the name l(4)102CDh by FlyBase.
The same problem arises with the l(4)19 name. The trouble is that there are
two different l(4)19 mutations: one is the old mutation described in 1964,
which in 1971 was renamed l(4)8b by Hochman and presumably later
l(4)102CDg3 by FlyBase; the other l(4)19 mutation was first published in
1971 and, accordingly, is not allelic to l(4)8. This mutation was given the
name l(4)102EFf by FlyBase. From the Bloomington as well as the Umeå Stock
Centers we have obtained the l(4)102CDg3 stock (# 1089 from Bloomington and
\# 73560 from Umeå). In both cases, this stock complements with l(4)8 and
maps to the region closest to the telomere. Therefore, we concluded that it
was the l(4)19 mutation described by Hochman in 1971 and not that described in
1964 to be allelic to l(4)8 and renamed l(4)8b in 1971 by Hochman! In our
paper, we used the name given by FlyBase and/or the Stock Center,
l(4)102CDg3. The mutation l(4)102EFf of FlyBase does not exist as stock in
the Stock Center. However, what the Stock Center carries as l(4)102CDg3
stock is more appropriately called l(4)102EFf, as we have shown, and
presumably corresponds to the l(4)19 mutation described and mapped to the
telomere by Hochman in 1971.
In summary, we know that (i) the 102CDh1 and 102CDh2 mutations (and
alleles of the Stock Center) are allelic and located between ey and toy as
described (Kronhamn et al., 2002); (ii) the l(4)102CDg1 allele is identical
to l(4)8, which never changed its name, and a toy allele with a headless
phenotype, which is why we called it toyhdl (Kronhamn et al., 2002); (iii)
the l(4)102CDg3 allele (and stock of the Stock Center) maps to the most
distal portion of the right arm of the 4th chromosome and hence is presumably
identical to the l(4)19 mutation mapped to the same region by Hochman in his
1971 paper. Therefore, this stock should be called more appropriately
l(4)102EFf, a name already carried by FlyBase for the most distal lethal
mutation on the right arm of the 4th chromosome.