Subject: FB-NG Help Mail: breakpoints of Df(3R)H-B79 comments: As part of a mapping project, we've used PCR to improve the localization of the breakpoints in Df(3R)H-B79. Since this Df stock is at Bloomington and is one of only a few in this region, I thought the info might be useful to others. Our data shows that the left breakpoint of Df(3R)H-B79 is between 92E8 and 92E9, near base 16272000 (just right of CG17208). The right breakpoint is between 92E12 and 92E13, near base 16330000 (just left of CG4323). We used primers designed to amplify specific genomic sequences and looked in homozygous Df embryos for (lack of) PCR product. realname: Dave Featherstone \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Dear Dave, thanks for this info \- so's I can record it for best use I need to be able to delimit which genes are deleted as well as those that are not. To confirm, in this case there is only one gene deleted, it being CG5115. Is that correct? Thanks for help, Rachel for FlyBase curators. \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Yes, CG5115 is deleted, but CG4323 may also be. \-Dave \-------------------------------------------------------------------- Subject: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Kevin, This is a DK3 (#4962). His results are very different from current bps (92B;92F13) and inconsistent with reports of failure to complement H at 92F3, bon at 92F2-3 and cdc2c at 92F10. Do you have any data for this one? \-- K \-------------------------------------------------------------------- Subject: Fwd: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Hi Dave-- I just did a polytene chromosome prep from our Df(3R)H-B79 stock, and I saw the same breakpoints that were reported in the literature. I didn't take the time to reanalyze the cytology down to single bands, but I confirmed that the proximal breakpoint is somewhere in 92B and the distal breakpoint is somewhere in 92F. I don't know how to reconcile this with your PCR results. Maybe the stock carries all or a portion of 92BF transposed to another region of the genome. A transposition could fail to complement H, bon, cdc2c, l(3)10585, Stat92E and CG17838, as reported, if these genes were subject to position effect variegation. I didn't look for an insertion of 92BE in the squashes, since I was looking at chromosomes from H-B79/TM2 larvae and the balancer makes this really hard to do. I'm reluctant to list this stock as a Tp instead of a Df without some other evidence. Best regards, Kevin \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Hi Kevin, All I can say is what our (my Tech's) PCR results were, which is what I forwarded via email. Chris Rodesch also did come complementation tests with H-B79 and said it complemented Stat92E, which is consistent with our PCR data (Although I later did this cross and concluded that B79 failed to complement Stat92E). Other than that, I can tell you nothing. We are unlikely to figure anything more out here since the H-B79 PCR was done while searching for a mutation that subsequently turned out to be in 92F4. Plus, I too hate TM2. I wrote because I thought our results might be handy additions to the annotation for H-B79, especially since they suggest the Df is smaller. I won't be offended at all if my note is associated with an 'editorial comment' noting that our PCR results don't mesh with other work and may be bogus. At least future researchers will have a heads up to look for themselves, hopefully resolve the matter, and write to Flybase. Anyway, it's your call. You guys do great work. \-Dave David E. Featherstone Department of Biological Sciences University of Illinois at Chicago SEL East, Room 4311 (Corner of Taylor & Halsted) 840 W. Taylor St. (M/C 067) Chicago, IL 60607 \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Dear all, This is all a bit odd as the PCR assessments would say that Df(3R)H-B79 doesn't even delete H. H is at coordinate 16447K or so and CG5115 (the only gene to be wholly deleted, according to the PCR data) is at coordinate 16309K or so. Stat92E is at 166371K or so. It is possible for the FlyBase aberrations data file to house statements about what is molecularly deleted and not deleted without these causing adjustments to statements about cytologically determined breakpoints. So I will curate your disussion as a pers comm from Dave and Kevin, and capture a. apparently contradictory data b. discussion of possibility of explanation \- and possibility of Tp. If there is to be confusion it is as well to document it well! . best to all, Rachel. \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Sounds fine to me. The PCR was done on the stock recently acquired from Bloomington. Chris Rodesch's comp tests were done when we were both in Kendal Broadie's lab in Utah, so used a previously-acquired stock. \-Dave \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 Hi Rachel-- It's fine with me to archive this discussion. The H-B79 stock does show a Hairless phenotype. Specifically, postvertical and orbital bristles are missing and wing vein L5 thins out as it approaches the wing margin. Thanks! Kevin \-------------------------------------------------------------------- Subject: Re: FB-NG Help Mail: breakpoints of Df(3R)H-B79 For what it's worth: I just checked our Df(3R)H-B79 stock, on which the PCR was performed, and it also is Hairless. And that, I agree, runs counter to the fact that we got PCR product from primers designed to amplify near base 16329k. \-Dave \--------------------------------------------------------------------
