Abstract
Several different strategies and materials were used for saturating the region 5q11.2–q13.3 with new, randomly distributed markers: isolation of human clones from three chromosome-5-specific libraries (a BssHII endclone phage library from the somatic cell hybrid H64 and two total genomic phage libraries from radiation hybrids IH12 and IH132), as well as Alu-PCR from chromosome-5-specific radiation hybrids with overlapping fragments in the region around the spinal muscular atrophy locus, followed either by direct isolation of Alu-PCR products or hybridization of Alu-PCR products to chromosome-5-gridded cosmid libraries. 253 human phage and cosmid clones were mapped to various parts of chromosome 5 by deletion mapping to somatic cell hybrid panels. 30 of these clones were mapped into the region 5q11.2–q13.3, 9 of which are flanking rate cutting BssHII-sites, known to be, often, starting points for genes. They represent excellent starting material for the development of new polymorphic markers and sequence-tagged sites, for YAC screening and building of contigs, as well as for direct isolation of genes.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
McKusick VA: Mendelian Inheritance in Man, ed 9. Baltimore, John Hopkins University Press, 1990 and ON LINE OMIM.
Brzustowicz LM, Lehner T, Castilla LH, Penchaszadeh GK, Wilhelmsen KC, Daniels R, Davies KE, Leppert M, Ziter F, Wood D, Dubowitz V, Zerres K, Hausmanowa-Petrusewicz I, Ott J, Munsat TL, Gilliam TC: Genetic mapping of chronic childhood-onset spinal muscular atrophy to chromosome 5q11.2–q13.3. Nature 1990;344:540–541
Melki J, Abdelhak S, Sheth P, Bachelot MF, Burlet P, Marcadet A, Aicardi J, Barois A, Carriere JP, Fardeau M, Fontan D, Ponsot G, Billette T, Angelini C, Barbosa C, Ferriere G, Lanzi G, Ottolini A, Babton MC, Cohen D, Hanauer A, Clerget-Darpoux F, Lathrop M, Munnich A, Frezal J: Gene for chronic proximal spinal muscular atrophies maps to chromosomes 5q. Nature 1990;344:767–768
Daniels RJ, Thomas NH, MacKinnon RN, Lehner T, Ott J, Flint TJ, Dubowitz V, Ignatius J, Donner M, Zerres K, Rietschel M, Cookson WOC, Brzustowicz LM, Gilliam TC, Davies KE: Linkage analysis of spinal muscular atrophy. Genomics 1992;12:335–339
Lien LL, Boyce FM, Kleyn P, Brzustowicz LM, Menninger J, Ward DC, Gilliam TC, Kunkel LM: Mapping of human microtubule-associated protein 1 B in proximity to the spinal muscular atrophy locus at 5q13. Proc Natl Acad Sci USA 1991;88:7873–7876
Brzustowicz LM, Kleyn PW, Boyce FM, Lien LL, Monaco AP, Penchaszadeh GK, Das K, Wang CH, Munsat TL, Ott J, Kunkel LM, Gilliam TC: Fine mapping of the spinal muscular atrophy locus to a region flanked by MAP1B and D5S6. Genomics 1992;13:991–998
Wirth B, Voosen B, Röhrig D, Knapp M, Piechaczek B, Rudnik-Schöneborn S, Zerres K: Fine mapping and narrowing of the genetic interval of the spinal muscular atrophy region by linkage studies. Genomics 1993;15:113–118
Michielis F, Burmeister M, Lehrach H: Derivation of clones close to met by preparative field inversion gel electrophoresis. Science 1987;236:1305–1307
Frischauf AM: Construction and use of linking libraries. Technique 1989;1:3–10
Poustka A, Pohl TM, Barlow DP, Frischauf AM, Lehrach H: Construction and use of human chromosome jumping libraries from NotI-digested DNA. Nature 1987;325:353–355
Varesco L, Thomas HJW, Cottrell S, Murday V, Fennell SJ, Williams S, Searle S, Sheer D, Bodmer WF, Frischauf AM, Solomon E: CpG island clones from a deletion encompassing the gene for adenomatous polyposis coli. Proc Natl Acad Sci USA 1989;86:10118–10122
Nelson DL, Ledbetter SA, Corbo L, Victoria MF, Ramirez-Solis R, Webster TD, Ledbetter DH, Caskey CT: Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci USA 1989;86:6686–6690
Ledbetter SA, Nelson DL, Warren ST, Ledbetter DH: Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequences polymerase chain reaction. Genomics 1990;6:475–481
Tagle DA, Collins F: An optimized Alu-PCR primer pair for human-specific amplification of YACs and somatic cell hybrids. Hum Mol Genet 1992;2:121–122
Monaco A, Lam VMS, Zehetner G, Lennon GG, Douglas C, Nizetic D, Goodfellow PN, Lehrach H: Mapping irradiation hybrids to cosmid and yeast artificial chromosome libraries by direct hybridization of Alu-PCR products. Nucleic Acids Res 1991;12:3315–1318
Gilliam TC, Freimer NB, Kaufmann CA, Powchik PP, Bassett AS, Bengtsson U, Wasmuth JJ: Deletion mapping of DNA markers to a region of chromosome 5 that cosegregates with schizophrenia. Genomics 1989;5:940–944
Wood S, Bernard LE: Mapping a 5q11.2–q13.3 deletion chromosome (abstract). Cytogenet Cell Genet 1992;61:233.
Charlock LR, Wasmuth JJ: Molecular approach to analyzing the human 5p deletion syndrome, Cri-du-chat. Somat Cell Mol Genet 1985:8:245–264.
Bishop DT, Westbrook C: Report of the committee on the genetic constitution of chromosome 5. Cytogenet Cell Genet 1990;55:111–117
Hudson TJ, Engelstein M, Lee MK, Ho EC, Rubinfeld MJ, Adams CP, Housman DE, Dracopoli NC: Isolation and chromosomal assignment of 100 highly informative human simple sequence repeat polymorphisms. Genomics 1992;13:622–629
Frischauf AM: Digestion of DNA: size fractionation: Construction and characterization of a genomic library. Methods Enzymol 1987;152:183–199
Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A laboratory manual, ed 2. Cold Spring Harbor, Cold Spring Harbor Laboratory Press, 1989.
Pohl TM, Zimmer M, MacDonald ME, Smith B, Bucan M, Poustka A, Volinia S, Searle S, Zehetner G, Wasmuth JJ, Gusella J, Lehrach H, Frischauf AM: Construction of a NotI linking library and isolation of new markers close to the Huntington’s disease gene. Nucleic Acids Res 1988;19:9185–9197
Rüther K, Wirth B: A new polymorphic probe on 5q11.2–q13.3: ECB306Bgl2.1 (D5S215). Nucleic Acids Res 1991;5:1160.
Wirth B, Pick E, Leutner A, Dadze A, Voosen B, Piechaczek-Wappenschmidt B, Knapp M, Rudnik-Schöneborn S, Schönling J, Cox S, Spurr N, Zerres K: Large linkage analysis in 100 families with autosomal recessive spinal muscular atrophy (SMA) and 11 CEPH-families using 15 polymorphic loci in the region 5q11.2–q13.3. Genomics, submitted.
Larsen F, Gundersen G, Lopez R, Prydz H: CpG islands as gene markers in the human genome. Genomics 1992;13:1095–1207
Germino GG, Weinstat-Saslow D, Himmelbauer H, Gillespie GAJ, Somlo S, Wirth B, Barton N, Harris KL, Frischauf AM, Reeders S: The gene for autosomal dominant polycistic kidney disease lies in a 750 kb CpG-rich region. Genomics 1992;13:144–151
Borrow J, Goddard AD, Sheer D, Solomon E: Molecular analysis of acute promyelocytic leukemia breakpoint cluster region on chromosome 17. Nature 1990;249:1577–1580
Acknowledgements
We cordially thank Drs. A.M. Frischauf and L. Varesco for the BssHII endclones, Dr. A.M. Frischauf for the gridded cosmid filters, U. Novicka for picking and sending the cosmids, and Dr. L. Deaven (Los Alamos) for making the chromosome-5-gridded cosmid library available. We also thank Drs. E. Solomon and H. Thomas for the PN/TS cell line and the RHs, and Dr. J. J. Wasmuth for the HHW1064 and HHW213 cell lines. This work was funded by the Deutsche Forschungsgemeinschaft.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Wirth, B., Schönling, J., El-Agwany, A. et al. Efficiency of Various Strategies and Materials to Generate New Markers: Saturating the Region 5q11.2–q13.3 with 30 New Randomly Distributed Clones. Eur J Hum Genet 1, 314–324 (1993). https://doi.org/10.1159/000472430
Received:
Revised:
Accepted:
Issue date:
DOI: https://doi.org/10.1159/000472430
