Abstract
Although advances in the development of positional cloning techniques have rapidly accelerated the pace of physical mapping and gene localization, the complete and efficient isolation of transcribed sequences from within large targeted genomic regions remains a significant challenge. Here, we describe two approaches used to isolate transcripts encoded within region Xp11.21. First, subcloned genomic fragments derived from regional YAC clones were used to identify evolutionarily conserved sequences (ECSs); ECSs were used to screen cDNA libraries and isolate regional transcripts. Second, YAC DNA was immobilized on a membrane and hybridized to PCR-amplified cDNA clone inserts; selectively retained inserts were subcloned to construct an enriched region-specific cDNA library. Both techniques were successfully used to isolate region-specific transcribed sequences. The advantages and limitations of each approach are discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
T. Ohta, and M. Kinura, Functional organization of genetic material as a product of molecular evolution, Nature 233:118 (1971).
W.A. Bickmore, and A.T. Sumner, Mammalian chromosome banding - an expression of genome organization, Trends Genet. 5:144 (1989).
E.M. Southern, Genome mapping: cDNA approaches, Current Opinion Genet. Devel. 2:412 (1992).
J.O. Bishop, The gene numbers game, Cell 2:81 (1974).
N.D. Hastie and J.O. Bishop, The expression of three abundance classes of messenger RNA in mouse tissues, Cell 9:761 (1976).
A.P. Monaco, R.L. Neve, F.C. Colletti, C.J. Bertelson, D.M. Kurnit, and L.M. Kunkel, Isolation of candidate cDNAs for portions of the Duchenne muscular dystrophy gene, Nature 323:646 (1986).
J.M. Rommens, M.C. Iannuzzi, B. Kerem, M.L. Drumm, G. Melmer, M. Dean, R. et al., Identification of the cystic fibrosis gene: chromosome walking and jumping, Science 245:1059 (1989).
A.P. Bird, CpG-rich islands and the function of DNA methylation, Nature 321:209 (1986).
L. Bonetta, S.E. Kuehn, A. Huang, D.J. Law, L.M. Kalikin, M. Koi, et al., Wilms tumor locus on 11p13 defined by multiple CpG island-associated transcripts, Science 250:994 (1990).
T. Yokoi, M. Lovett, Z.Y. Cheng, and C.J. Epstein, Isolation of transcribed DNA sequences from chromosome 21 using mouse fetal cDNA, Hum. Genet. 74:137 (1986).
U. Hochgeschwender, J.G. Sutcliffe, and M.B. Brennan, Construction and screening of a genomic library specific for mouse chromosome 16, Proc. Natl. Acad. Sci. USA 86:8482 (1989).
G.M. Duyk, S.W. Kim, R.M. Myers, and D.R. Cox, Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA, Proc. Natl. Acad. Sci. USA 87:8995 (1990).
A.J. Buckler, D.D. Chang, S.L. Graw, J.D. Brook, D.A. Haber, P.A. Sharp, and D.E. Housman, Exon amplification: a strategy to isolate mammalian genes based on RNA splicing, Proc. Natl. Acad. Sci. USA 88:4005 (1991).
M. Lovett, J. Kere, and L.M. Hinton, Direct selection: a method for the isolation of cDNAs encoded by large genomic regions, Proc. Natl. Acad. Sci. USA 88:9628 (1991).
S. Parimoo, S.R. Patanjali, H. Shukla, D.D. Chaplin, and S.M. Weissman, cDNA selection: efficient PCR approach for the selection of cDNAs encoded in large chromosomal DNA fragments, Proc. Natl. Acad. Sci. USA 88:9623 (1991).
J.L. Gorski, M. Boehnke, E.L. Reyner, and E.N. Burright, A radiation hybrid map of the proximal short arm of the human X chromosome spanning incontinentia pigmenti 1 (IP1) translocation breakpoints, Genomics 14:657 (1992).
J.L. Gorski, E.N. Burright, E.L. Reyner, P.N. Goodfellow, and D.L. Burgess, Isolation of DNA markers from a region between incontinentia pigmenti 1 (IP1) X-chromosomal translocation breakpoints by a comparative PCR analysis of a radiation hybrid subclone mapping panel, Genomics 14:649 (1992).
E.N. Burright, N.G. Pasteris, and J.L. Gorski, (unpublished results).
P.D. Cotter, H.F. Willard, J.L. Gorski, and D.F. Bishop, Assignment of human erythroid deltaaminolevulinate synthase (ALAS2) to a distal subregion of band Xp11.21 by PCR analysis of somatic cell hybrids containing X;autosome translocations, Genomics 13:211 (1992).
J.L. Gorski, E.N. Burright, C.E. Hamden, C.K. Stein, T.W. Glover, and E.L. Reyner, Localization of DNA sequences to a region within Xp11.21 between incontinentia pigmenti type 1 (IP1) X-chromosomal translocation breakpoints, Am. J. Hum. Genet. 48:53 (1991).
T.W. Glover, V. Verga, J. Rafael, J.L. Gorski, E. Bawle, and J.V. Higgins, Translocation breakpoint in Aarskog syndrome maps to Xp11.21 between ALAS2 and DXS323, Hum. Mol. Genet. 2:1717 (1993).
T. Maniatis, E.F. Fritsch, and J. Sambrook, “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory, Cold Spring Harbor, (1982).
E.N. Burright, B.J. Trask, and J.L. Gorski, Incontinentia pigmenti type 1 (IP1) gene cloned in yeast artificial chromosomes: (in preparation).
N.G. Pasteris, M. Bilecki, and J.L. Gorski, YAC subclone contig assembly by serial interspersed repetitive sequence (IRS)-PCR product hybridizations, Nucl. Acids Res. (in press).
P.G. Sealey, P.A. Whittaker, and E.M. Southern, Removal of repeated sequences from hybridization probes, Nucl. Acids Res. 13:1905 (1985).
D. Vetrie, I. Vorechovsky, P. Sideras, J. Holland, A. Davies, F. Flinter, L. Hammarstrom, et al.,The gene involved in X-linked agammaglobulinaemia is a member of the src family of protein-tyrosine kinases, Nature 361:226 (1993).
J.M. Rommens, B. Lin, G.B. Hutchinson, S.E. Andrew, Y.P. Goldberg, M.L. Glaves, et al., A transcription map of the region containing the Huntington disease gene, Hum. Mol. Genet. 2:901 (1993).
W-F. Fan, X. Wei, H. Shukla, S. Parimoo, H. Xu, P. Sankhavaram, Z. Li, S.M. Weissman, Application of cDNA selection techniques to regions of the human MHC, Genomics 17:575 (1993).
F.S. Collins, Positional cloning: let’s not call it reverse anymore, Nature Genetics 1:3 (1992).
F.S. Collins, and D. Galas, A new five-year plan for the U.S. Human Genome Project, Science 262:43 (1993).
Z. Sedlacek, D.S. Konecki, R. Siebenhaar, P. Kioschis, and A. Poustka, Direct selection of DNA sequences conserved between species, Nucl. Acids Res. 21:3419 (1993).
L. Carroll, “Alice’s Adventures in Wonderland & Through the Looking-Glass,” Ninth Printing, The New American Library, New York (1960).
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Springer Science+Business Media New York
About this chapter
Cite this chapter
Burright, E.N., Pasteris, N.G., Bialecki, M.D., Gorski, J.L. (1994). Use of cDNA Selection and Evolutionarily Conserved Sequences to Isolate Transcribed Sequences from Region Xp11.21. In: Hochgeschwender, U., Gardiner, K. (eds) Identification of Transcribed Sequences. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-2562-2_3
Download citation
DOI: https://doi.org/10.1007/978-1-4615-2562-2_3
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4613-6094-0
Online ISBN: 978-1-4615-2562-2
eBook Packages: Springer Book Archive