Abstract
Tuberous sclerosis (TSC) is a heterogeneous multisystem disorder with loci on 9q34 (TSC1) and 16p13.3 (TSC2). The TSC2 gene has recently been isolated, while the TSC1 gene has been mapped to a 5-cM region between the markers D9S149 and D9S114. In our effort to localise and clone TSC1, we have obtained three adjacent cosmid contigs that cover the core of the candidate region. The three contigs comprise approximately 600 kb and include 80 cosmids, 2 P1 clones, 1 YAC, 5 anonymous markers and 4 sequence-tagged sites. The ABO blood group locus, the Surfeit gene cluster, the dopamine β-hydroxylase gene (DBH) and VAV2, a homologue of the vav oncogene, have all been mapped within the contigs. Exon trapping and mutation screening experiments, aimed at identifying the TSC1 gene, are currently in progress.
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Introduction
Tuberous sclerosis (TSC) is an autosomal dominant multisystem disorder. The brain, skin, heart and kidneys are often affected and almost all other tissues and organs may be involved, except muscle syncytia [1]. The disease shows a high penetrance with variable expression and is known for its locus heterogeneity, with one locus mapping to chromosome 9q34 (TSC1) and another to chromosome 16p13.3 (TSC2) [2]. The number of families linked to each locus is approximately equal and there is no significant evidence for a third locus [3]. The TSC2 gene has been isolated [4] and both genes may act as growth or tumour suppressors, since loss of heterozygosity (LOH) has been demonstrated on 9q34 [57] or 16p 13 [7] in various hamartomatous tissues from patients with TSC.
The chromosome 9 locus for tuberous sclerosis, TSC1, is tightly linked to the ABO blood group locus [8] and maps in a gene-rich region on chromosome 9q34. Since the initial linkage report by Fryer et al. [8], the TSC1 region has been refined to a region of 5 cM between D9S149 and D9S114 [3, 9–14]. However, there is no consensus on the exact position of TSC1 within this interval, since some groups have found recombinants in favour of a position proximal to ABO and the dopamine β-hydroxylase gene (DBH), while other groups have presented data supporting a location distal to these markers [15]. The conflicting observations have several possible causes, including misclassification of individuals with only minor clinical findings or non-linkage of one or more families.
Several genes have been mapped within the TSC1 candidate region, including ABO, DBH, the Surfeit gene cluster and VAV2 [16–18], while other disorders genetically linked to ABO include torsion dystonia [19] and nail patella syndrome [20, 21].
In this paper we present the results of a contig assembly and gene mapping effort, focused on part of the TSC1 candidate region around ABO and DBH. Our detailed map spans 600 kb, corresponding to more than 2 cM of the TSC1 critical region. Eight genes and several known and novel genetic markers have been precisely positioned on a genomic EcoRI map between D9S149 and D9S114.
Materials and Methods
Libraries
The ICI YAC library [22] was accessed through the UK Human Genome Mapping Resource Centre and sets of primary, secondary and tertiary pools for PCR screening were provided by R. Elaswarapu. Primary pools from the St. Louis YAC library [23] were supplied by J. den Dunnen from the Department of Human Genetics in Leiden. The P1 library was made from human foreskin fibroblast DNA [24]. The library was gridded into 125 96-well plates with approximately 12 different P1 clones per well and pools were made for PCR screening. The chromosome-9-specific cosmid library LL09NC01‘P’ was constructed at the Biomedical Sciences Division, LLNL, Livermore, Calif., USA under the auspices of the National Laboratory Gene Library Projects sponsored by the US Department of Energy. The library was replicated on gridded filters as described [25] at the YAC screening core of the Department of Human Genetics in Leiden. Two sets of membranes were used to make pools for PCR screening [26]. The nomenclature of the cosmids in the contigs is the same as the nomenclature of the library source from which they were obtained. Cosmid ABO17 was provided by J. Wolfe.
Cosmid Library Screening
Hybridisation probes were generated by inter-Alu PCR [27] using primers CL1 and CL2 [28] or by isolating end fragments from cosmids in low-melting agarose. Probes were randomly labelled, competed with total human DNA, hybridised to nylon filters and washed using standard procedures [29]. Cosmid library screening by PCR was performed by screening two-dimensional pools of clones as described by Green and Olson [30].
YACs, P1 and Cosmid Clones
Cosmid and P1 DNA was prepared, isolated and fingerprinted using standard techniques [29]. YACs, P1 and cosmid clones were mapped back to 9q34 by fluorescence in situ hybridisation (FISH) [31].
Sequence-Tagged Sites (STSs)
STSs were developed by YAC end rescue inverse PCR or direct sequencing of cosmids. YAC end rescue was performed as described by Silverman et al. [32] and the products were sequenced directly. The Sequence was derived from the cosmid clones by cycle sequencing (Pharmacia) with the appropriate vector primers.
Results and Discussion
Strategy
We aimed to isolate a significant part of the TSC1 critical region between the markers D9S149 and D9S114 on 9q34. Several additional markers are known to map between these two, but have not been convincingly associated with genuine recombination events. The initial strategy was to isolate the region in YACs, P1 and cosmid clones. However, attempts to obtain YACs were hampered by underrepresentation of the region in the available libraries. This prompted us to follow an alternative strategy which consisted of cosmid walking complemented by screening P1 libraries.
YAC Library Screening
Two YACs from the ICI library, 4DD1 (120 kb) and 25DG9 (320 kb), were identified with primers specific for the ABO locus. STS mapping using primer pairs from both ends of the YACs indicated that the left ends of both inserts overlapped; however, inter-Alu PCR in combination with hybridisation experiments suggested that the region of overlap was small. FISH analysis confirmed the localisation of both YACs to chromosome 9q34; however, 25DG9 gave an additional signal on chromosome 18 indicating chimerism. This clone was not investigated further. No additional YACs were identified in the ICI library using the end clone STSs from 4DD1 or 25DG9, or with additional markers from the TSC1 candidate region (D9S10, D9S66, DBH). An STS derived from the left arm of YAC 4DD1 was used to screen the St. Louis YAC library and identified two duplicate clones, 51A7 and 61A10 (200 kb). FISH analysis mapped 51A7 to 9qter; however, STS mapping experiments using primers derived from the right arm of this clone suggested that it contained a large deletion (data not shown) and it was not investigated further. It is interesting to note that the TSC2 locus on chromosome 16 was also found to be underrepresented in YAC libraries [unpubl. results].
Contig Assembly
Starting points for cosmid contig assembly were ABO, DBH and D9S10 (fig. 1). Cosmids were identified with both the left and right end clones of YAC 4DD1 and two contigs were constructed of 110 and 130 kb, respectively (fig. 2, contigs A and B). The orientation of the cosmid contigs was consistent with results from YAC inter-Alu PCR screening of to cosmid library and with the YAC STS mapping experiments. No cosmids could be identified distal to cosmid 255A6 (contig B). Only a single non-rearranged cosmid and a single P1 clone were detected at the ABO locus, and no clone could be detected linking the two contigs. However, from the size of the 4DD1 YAC and direct visual hybridisation (DIRVISH) experiments of streched DNA [33] [unpubl. results], we estimated that the gap is approximately 30 kb.
Cosmids were identified with the DBH cDNA and probe pMCT136 from the D9S10 locus. DBH and D9S10 map 1 and 2 cM distal to ABO, respectively, and were linked by chromosome walking, covering a physical distance of 150 kb (contig C). This indicates that the genetic versus physical distance ratio in this region is large. The contig was extended proximal of DBH by 125 kb, but could not be extended further towards ABO. We did isolate a P1 clone with an STS from the proximal end of 251C9, but could not bridge the gap. The distance between clone 251C9 (contig B) and 255A6 (contig C) could not be resolved by interphase FISH, indicating that the gap between contigs B and C is small. DIRVISH DNA mapping experiments are in progress to estimate the size of the gap.
In regions of overlap, the contigs presented here were consistent with the cosmid contigs constructed by HinfI fingerprinting as described by Nahmias et al. [34]. They need at least 50% overlap between cosmids before the clones are joined in a contig. Our data are more detailed and detect smaller overlaps. Additional cosmids have been isolated from the flanking locus D9S149. Chromosome-walking experiments are currently focused on closing the gap between D9S149 and the most proximal ABO contig (contig A).
Mapping of Markers and Genes in the Contigs
RFLPs and unique STSs are listed in tables 1 and 2. The STSs 180G3-T3 and 4DD1L map to adjacent EcoRI fragments in contig A. Two additional STSs, 4DD1R and 251C9-T3 were mapped to contigs B and C, respectively. Existing minisatellite repeats (D9S122 and D9S150) [13] were precisely positioned within this contig (fig. 2, contig C) and a HindIII polymorphism (D9S968) was detected immediately proximal of DBH.
The position and orientation, where known, of genes identified within the contigs are indicated in figure 2. The role and expression pattern of the ABO blood group transferase indicate that it is not a good candidate for TSC1. The Surfeit gene cluster had been previously mapped by in situ hybridisation telomeric to the c-abl and can genes on 9q34 [35]. A oligonucleotide derived from the Surf-3 cDNA sequence detected a 1.2-kb EcoRI fragment in several cosmids, slightly distal to ABO in contig B. Cosmid 255A6 was digested with XbaI to orientate the cluster in the map. In the mouse this cluster consists of 6 housekeeping genes, which are unrelated by sequence homology [35]. To date, the Surfeit genes form the tightest gene cluster known in mammals. Since these genes are in the critical region of TSC1 and not much is known about their function, mutation analysis in TSC patients must be considered.
Our EcoRI mapping data from the DBH locus is consistent with that of Kobayashi et al. [36]. The direction of transcription is towards the telomere. The role of DBH in the conversion of dopamine to noradrenaline and the neurological manifestations of TSC led to the proposal that DBH could be a candidate for the TSC1 gene [37]. However, more recent results suggest that TSC1 maps either distal or proximal to DBH and consequently DBH is not such an attractive candidate.
Exon trapping [38] efforts using our cosmids from the D9S10 locus identified a gene homologous to the vav oncogene [16]. This gene, designated VAV2, was considered a good candidate for the TSC1 gene. However, intensive screening failed to identify any mutations, and VAV2 was consequently excluded as a candidate gene for TSC1 [16, 17].
Eight different genes could be placed on the map. The region is gene dense and although some genes map extremely close to each other, we cannot exclude the presence of other, as yet unidentified, expressed sequences in the same region. Experiments to identify and characterise additional genes from the TSC1 candidate region are in progress.
Further efforts are being directed towards extending the contigs and screening TSC patients for mutations by pulsed-field gel electrophoresis using novel probes derived from our cloned material. The identification of large deletions at the TSC2 locus made a significant contribution to the rapid isolation of the TSC2 gene [4].
In conclusion, we have identified 80 cosmids, 2 P1 clones and a single non-rearranged YAC from the TSC1 candidate region on 9q34. We have constructed a detailed restriction map of three adjacent cosmid contigs and oriented the maps with respect to known and previously unidentified genes and DNA markers. We have shown that DBH and D9S10, previously estimated to be 1 cM apart, are separated by less than 300 kb, and estimate that the physical distance between ABO and DBH is less than 300 kb.
In conjunction with the accompanying article [34], we have shown that cosmid walking, using a large chromosome-specific cosmid library can provide almost complete coverage of a large genomic region. This minimises the need to search for non-chimeric non-rearranged YAC clones, which have been difficult to obtain from the TSC1 region. Moreover, our contigs and the associated maps provide a good tool for generating novel markers and cloning additional genes from this region. It would be of great help to get more excluding data on the recombinants within the region, so that the search for TSC1 can be restricted to a smaller area. LOH studies in tumours of patients and the development of new polymorphic CA repeats in the area, especially between ABO and D9S149, could help reduce the critical region. Ultimately, it is hoped that this work will lead to the identification of the TSC1 gene.
References
Gomez MR: Tuberous Sclerosis, ed 2. New York, Raven Press, 1988.
Kandt RS, Haines JL, Smith M, Northrup H, Gardner RJM, Short MP, Dumars K, Roach ES, Steingold S, Wall S, Blanton SH, Flodman P, Kwiatkowski DJ, Jewell A, Weber JL, Roses AD, Pericak-Vance MA: Linkage of an important gene locus for tuberous sclerosis to a chromosome 16 marker for polycystic kidney disease. Nature Genet 1992;2:37–41
Janssen B, Sampson J. van der Est M, Deelen W, Verhoef S, Daniels I, Hesseling A, Brook-Carter P, Nellist M, Lindhout D, Sandkuijl L, Halley D: Refined localization of TSC1 by combined analysis of 9q34 and 16p13 data in 14 tuberous sclerosis families. Hum Genet 1994;94:437–440
The European Chromosome 16 Tuberous Sclerosis Consortium: Identification and characterisation of the tuberous sclerosis gene on chromosome 16. Cell 1993;75:1305–1315
Carbonara C, Longa L, Grosso L, Borrone C, Garrè M. Brisigotti M, Migone N: 9q34 loss of heterozygosity in a tuberous sclerosis astrocytoma suggests a growth suppressorlike activity also for the TSC1 gene. Hum Mol Genet 1994;3:1829–1832.
Green AJ, Johnson PH, Yates JRW: The tuberous sclerosis gene on chromosome 9q34 acts as a growth suppressor. Hum Mol Genet 1994;3:1833–1834
Green AJ, Smith M, Yates JRW: Loss of heterozygosity on chromosome 16p13.3 in hamartomas from tuberous sclerosis patients. Nat Genet 1994;6:193–196
Fryer AE, Chalmers A, Connor JM, Fraser I, Povey S, Yates AD, Yates JRW, Osborne JP: Evidence that the gene for tuberous sclerosis is on chromosome 9. Lancet 1987;i:659–661
Connor JM, Pirrit LA, Yates JRW, Fryer AE, Ferguson-Smith MA: Linkage of the tuberous sclerosis locus to a DNA polymorphism detected by c-abl. J Med Genet 1987;24:544–546.
Haines JL, Short MP, Kwiatkowski DJ, Jewell A, Andermann E, Bejjani B, Yang CH, Gusella JF, Amos JA: Localization of one gene for tuberous sclerosis within 9q32–9q34, and further evidence for heterogeneity. Am J Hum Genet 1991;49:764–772
Northrup H, Kwiatkowski DJ, Roach ES, Dobyns WB, Lewis RA, Herman GE, Rodriguez E, Daiger SP, Blanton SH: Evidence for genetic heterogeneity in tuberous sclerosis: One locus on chromosome 9 and at least one locus elsewhere. Am J Hum Genet 1992;51:709–720
Sampson JR, Janssen LAJ, Sandkuijl LA and the Tuberous Sclerosis Collaborative Group: Linkage investigation of three putative tuberous sclerosis determining loci on chromosome 9q, 11q and 12q. J Med Genet 1992;29:861–866
Povey S, Armour J, Farndon P, Haines JL, Knowles M, Olopade F, Pilz A, White JA, members of the Utah Genome Center Genetic Marker and Mapping Group, Kwiatkowski DJ: Report on the Third International Workshop on Chromosome 9. Ann Hum Genet 1994;58:177–250
Janssen LAJ, Sandkuyl LA, Merkens EC, Maat-Kievit JA, Sampson JR, Fleury P, Hennekam RCM, Grosveld GC, Lindhout D, Halley DJJ: Genetic heterogeneity in tuberous sclerosis. Genomics 1990;8:237–242
Sampson JR, Harris PC: The molecular genetics of tuberous sclerosis. Hum Mol Genet 1994;3:1477–1480
Kwiatkowski DJ, Short MP, Jozwiak S, Bovey CM, Ramlakhan S, Haines JL, Henske EP: Identification of VAV2 on 9q34 and its exclusion as the tuberous sclerosis gene TSC1. Ann Hum Genet 1995;59:25–37
Smith M, Brickey W, Handa K, Gargus JJ: Sequence analysis of MCT 136 (locus D9S10) in the TSC gene region reveals amino acid domains with sequence homology to RAS activating signal molecules VAV and HSOS. Ann Hum Genet 1994;58:235–236
Woodward KJ, Nahmias J, Hornigold N, West L, Pilz AJ, Kwiatkowski DJ, Benham F, Wolfe J, Povey S: Mapping chromosome 9q34 by FISH using metaphase chromosomes with specific translocation breakpoints. Ann Hum Genet 1994;58:241–242
Ozelius L, Kramer PL, Moskowitz CB, Kwiatkowski DJ, Brin MF, Bressman SB, Schuback DE, Falk CT, Risch N, de Leon D, Burke RE, Haines J, Gusella JF, Fahn S, Breakfield XO: Human gene for torsion dystonia located on chromosome 9q32–q34. Neuron 1989;2:1427–1434
Renwick JH, Lawler SD: Genetical linkage between the ABO and nail-patella loci. Ann Hum Genet 1955;19:312–331
Renwick JH, Schulze J: Male and female recombination fractions for the nail patella: ABO linkage in man. Ann Hum Genet 1965;28:379–392
Anand R, Riley JH, Butler R, Smith JC, Markham AF: A 3.5 genome equivalent multi access YAC library: Construction, characterisation, screening and storage. Nucleic Acids Res 1990;18:1951–1956
Burke DT, Carle GF, Olson MV: Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science 1987;236:806–812
Pierce JC, Sauer B, Sternberg N: A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: Improved cloning efficacy. Proc Natl Acad Sci USA 1992;89:2056–2060
Bentley DR, Todd C, Collins J, Holland J, Dunham I, Hassock S, Bankier A, Giannelli F: The development and application of automated gridding for efficient screening of yeast and bacterial ordered libraries. Genomics 1992;12:534–541
Kwiatkowski DJ, Zoghbi HY, Ledbetter SA, Ellison KA, Chinault AC: Rapid identification of yeast artificial chromosome clones by matrix pooling and crude lysate PCR. Nucleic Acids Res 1993;18:7197–7203
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
Lengauer C, Riethman HC, Speicher MR, Taniwaki M, Konecki D, Green ED, Becher R, Olson MV, Cremer T: Metaphase and interphase cytogenetics with Alu-PCR-amplified yeast artificial chromosome clones containing the BCR gene and the protooncogene c-raf-1, c-fins and c-erbB-2 Cancer Res 1992;52:2590–2596.
Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manuel, ed. 2. Cold Spring Harbor, Cold Spring Harbour Press, 1989.
Green ED, Olson MV: Systematic screening of yeast artificial-chromosome libraries by use of the polymerase chain reaction. Proc Natl Acad Sci USA 1990;87:1213–1217
Breen M, Arveiler B, Murray I, Gosden JR, Porteous DJ: YAC mapping by FISH using Alu-PCR-generated probes. Genomics 1992;13:726–730
Silverman GA, Jockel JI, Domer PH, Mohr RM, Taillon-Miller P, Korsmeyer SJ: Yeast artificial chromosome cloning of a two-megabase-size contig within chromosomal band 18q21 establishes physical linkage between BCL2 and plasminogen activator inhibitor type 2. Genomics 1991;9:219–228
Wiegant J, Kalle W, Mullenders L, Brookes S, Hoovers JMN, Dauwerse JG, van Ommen GJB, Raap AK: High-resolution in situ hybridisation using DNA halo preparations. Hum Mol Genet 1992;1:587–591
Nahmias J, Hornigold N, Fitzgibbon J, Woodward K, Pilz A. Griffin D. Henske EP, Nakamura Y, Graw S, Florian F, Benham F, Povey S, Wolfe J: Cosmid contigs spanning 9q34 including the TSC1 candidate region. Eur J Hum Genet 1995;3:65–77
Yon J. Jones T, Garson K, Sheer D, Fried M: The organization and conservation of the human Surfeit gene cluster and its localization telomeric to the c-abl and can proto-oncogenes at chromosome band 9q34.1. Hum Mol Genet 1993;2:237–240
Kobayashi K, Kurosawa Y, Fujita K, Nagatsu T: Human dopamine beta hydroxylase gene: Two mRNA types having different 3′ terminal regions are produced through alternative polyadenylation. Nucleic Acids Res 1989;17:1089–1102
Janssen LAJ. Nellist M, Eussen BE, Ramlakhan S, Sampson JR, Hesseling-Janssen ALW, Verhoef S, Lindhout D, Halley DJJ: The map position of three candidate genes for tuberous sclerosis 1: XPAC, DBH and TAN1. Cytogenet Cell Genet 1993;64:115.
Buckler AJ, Chang DD, Graw SL, Brook JD, Haber DA, Sharp PA, Housman DE: Exon amplification: A strategy to isolate mammalian genes based on RNA splicing. Proc Natl Acad Sci USA 1991;88:4005–4009
Acknowledgements
We are grateful to Professors H. Galjaard and D. Lindhout for their continuous support. We would like to thank Dr. S. Povey, Dr. J. Wolfe, Joseph Nahmias and co-workers for sharing unpublished data and for their cooperation. This work was funded by the Dutch Organisation for Scientific Research (NWO).
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van Slegtenhorst, M., Janssen, B., Nellist, M. et al. Cosmid Contigs from the Tuberous Sclerosis Candidate Region on Chromosome 9q34. Eur J Hum Genet 3, 78–86 (1995). https://doi.org/10.1159/000472280
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DOI: https://doi.org/10.1159/000472280