Personal Communication from: Sandy Bernstein, Shuxing Zhang San Diego State University San Diego, CA Date: Nov. 18, 1999 Query from curator: I am working on the annotation of the Mhc genomic sequences from BDGP. I would like to be able to put as many complete mRNAs and CDSs on the sequence as possible but have only found the structures of six completely characterized mRNAs in the literature. I have found reference to the mRNAs containing the following variable exons (In the nomenclature of George et al. which I came accross first) in the literature From George et al. 1989 1) 3b, 7a, 9b, 11d, 15b 2) 3b, 7d, 9b, 11b, 15a From Wells et al. 1996 3) 3a, 7a, 9b, 11c, 15b 4) 3b, 7a, 9b, 11c, 15b 5) 3a, 7a, 9c, 11d, 15b 6) 3b, 7a, 9b, 11a, 15b All of the above use exons 17 and 19 and do not contain exon 18. In the Bernstein and Milligan JMB 1997 paper, it says that 12 combinations of alternative exons are known. If you could provide me with the structure of the additional complete forms, I will include them in the annotation. Also, a point of clarification: Am I interpreting the statement in Wells et al. "Note that the exon 11 series is designated in linear order as a-e, rather than by the order used in George et al. (1989)" correctly to mean that the correspondence between the exons in the Wells et al. and the George et al. papers is as follows? George et al. Wells et al. 11e 11a 11a 11b 11b 11c 11c 11d 11d 11e One last question. I am also including the positions of as many mutations, insertions, etc. as I can in the sequence. In Kronert et al. 1999. J.Cell Biol. 144(5):989-1000, the positions of the mutations in Table 1 are given in terms of the numbering of the chicken amino acid sequence. As a result, I am having a hard time locating them in the Drosophila sequence. In all cases, I have found the appropriate residue or residues within 4 amino acids of the stated position in the chicken sequence but don't know if these are the correct positions. In one case (Mhc[D45] there are two possible Ala codons (GCT) within three amino acid positions aa 261 (the stated position). I have tentatively mapped the mutations to the following Drosophila codons: Mhc mutation chick codon Drosophila codon (?) D1 625 623 D41 328 324 D45 261 258 0r 260 D62 638 (start) 637 (start) 5 200 200 8 832 829 Can you either confirm these positions or point me to a good source for the chicken numbering you are using? Reply: 1) The isoform compilation is in Table 2 from a manuscript we are preparing. Note that some are derived from cDNAs, others are from in situ hybridization. You probably don't want to list all the details of the embryonic forms. Probably somatic, cardiac, visceral or pharyngeal muscle would be the best description. Listing the new ones as "personal communication" would be OK (the co-author on the manuscript is Shuxing Zhang). 2) Your exon 11 designations are correct. Note, however, that Charlie Emerson is adamant that we use the George et al designations since they were published first. We are now doing so. Thus the table I attached uses the George designations. I suggest you use George et al's nomenclature, since this is what I have agreed to do. 3) The numbers you cite for the Drosophila mutations are correct. D45 should be Drosophila codon 258. Text version of Table 2 Stage and Tissue-specific use of Mhc Alternatative Exons in Drosophila Alternative Exons used in Embyonic Muscles/ cDNAs Mhc form Exons 3a, 7a, 9b, 11c, 15b, 18 excluded Tissues/cDNA Dorsal Acute 3 Longitudinal Oblique Lateral Longitudinal 1 Lateral Oblique Ventral Longitudinal 1-4 Segment Border Dorsal Oblique 3, 4, 5 Ventral Oblique 1, 2, 4-6 Embryonic cDNA c21 Mhc form Exons 3b, 7a, 9b, 11c, 15b, 18 excluded Tissues/cDNA Ventral Acute 3 Dorsal Acute 3 Dorsal Oblique 1, 2, 3 Segment Border Embryonic cDNA c61 Mhc form Exons 3a, 7a, 9b, 11d, 15b, 18 excluded Tissues/cDNA Dorsal Acute 1, 2 Ventral Oblique 1-6 Heart Cardiobast Mhc form Exons 3b, 7a, 9c, 11d, 15b, 18 excluded Tissues/cDNA Transverse (all 6) Dorsal Acute 1, 2 Mhc form Exons 3a, 7a, 9c, 11d, 15b, 18 excluded Tissues/cDNA Dorsal Acute 1, 2 Embryonic cDNA c52 Mhc form Exons 3b, 7a, 9c, 11c, 15b, 18 excluded Tissues/cDNA Ventral Acute 1, 2 Mhc form Exons 3a, 7b, 9b, 11d, 15b. 18 excluded Tissues/cDNA Pharyngeal Mhc form Exons 3b, 7a, 9b, 11a, 15b, 18 excluded Tissues/cDNA Embryonic cDNA c51 Alternative Exons used in Pupal and Adult Muscles/ cDNAs Mhc form Exons 3b, 7d, 9a, 11e, 15a, 18 included Tissues/cDNA Indirect flight muscle Mhc form Exons 3b, 7d, 9a, 11b, 15a, 18 included Tissues/cDNA Jump muscle-small cells Mhc form Exons 3b, 7d, 9a,b 11b, 15a, 18 included Tissues/cDNA Jump muscle-large cells Mhc form Exons 3b, 7d, 9b 11b, 15a, 18 included Tissues/cDNA Direct flight muscle #51 Mhc form Exons 3b, 7a, 9b 11c, 15b, 18 excluded Tissues/cDNA Direct flight muscle #52 Esophagus (adult) Mhc form Exons 3 N.A., 7 N.A., 9b, 11 N.A., 15a,b, 18 excl./incl. Tissues/cDNA Leg Mhc form Exons 3 N.A., 7 N.A., 9b, 11 N.A., 15a,b, 18 excluded Tissues/cDNA Proboscis Mhc form Exons 3 N.A., 7 N.A., 9b or c, 11 N.A., 15b, 18 excluded Tissues/cDNA Body wall Mhc form Exons 3b, 7d, 9b 11b, 15a, 18 excluded Tissues/cDNA Pupal cDNA cD301 Mhc form Exons 3-, 7a, 9b 11d, 15b, 18 excluded Tissues/cDNA Pupal cDNA cD302 Table 2 legend: N.A., not analyzed. Embryonic tissue localization from the present study. Embryonic cDNAs from Edwards (1990) and Wells et al., 1996. Pupal/adult tissue localization from Kazzaz and Rozek (1989), Collier, et al. (1990), Edwards (1990), Hastings and Emerson (1991), Kronert et al. (1991). Pupal cDNA clones are from George et al., 1989.
