A 2-Megabase Physical Contig Incorporating 43 DNA Markers on the Human X Chromosome at p11.23–p11.22 from ZNF21 to DXS255

Km, Boycott; Gr, Halley; Schlessinger, David; Nt, Bech-Hansen

doi:10.1006/geno.1996.0224

Cited by 12 publications

(20 citation statements)

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“…However, this YAC identifies the cosmid (LLNLc110C1459) that contains DXS1039, indicating only a small deletion within it. Another YAC that overlaps with the cosmid contig (yWXDF14D4, Boycott et al 1996) contains the markers DXS6666, DXS1039, DXS1426, and DXS1416. In addition, comparative hybridization of the LL cosmid library with the YACs ICRFy900B0617 and yWXDF14D4 revealed >10 overlapping clones.…”

Section: Toward a Cosmid Contig Connecting The Loci Dxsi03? And Dxs255mentioning

confidence: 99%

“…Overlap of the YAC ICRFy900B0617 with the YAC yWXDA39E7 (Boycott et al 1996) was first demonstrated by PCR reactions with the markers DXS8222 (Boycott et al 1996) and DXS6850 and second by hybridization of the LL cosmid library revealing six overlapping clones. In addition, three of the cosmid clones found by the YAC yWXDA39E7 are identical with the cosmid clones identified by hybridization with the probe M27[3 (data not shown).…”

Section: Toward a Cosmid Contig Connecting The Loci Dxsi03? And Dxs255mentioning

confidence: 99%

“…In addition, most YACs isolated from various libraries subsequently have proven to be either chimeric, unstable, or very LONG-RANGE MAP OF A 3.5-MB REGION IN XP! 1.23-22 small Kwan et al 1995a,b;Boycott et al 1996), making it difficult to construct an accurate physical map. The YACs previously used to connect OATL1 with GF-1 were not reliable as the YAC ICRFy900F0501 Fisher et al 1995) and YAC ICI-27GF2 (Derry et al 1994(Derry et al , 1995aFisher et al 1995), both unstable and chimeric.…”

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

“…Instability has also been shown for the YAC ICRFy900E021, which has been used previously to connect TFE-3 and SYP (Hagemann 1994). The central and distal parts of the region between ZNF21 and DXS2SS have been especially difficult to clone in YACs in one study, with overall rates of 30% chimerism and 40-80% internal deletions (Boycott et al 1996). The only stable and reliable YACs for this region thus far are quite small (<200 kb) and were isolated either from an X chromosome-specific YAC library (Lee et al 1992) or from the St. Louis YAC library (Boycott et al 1996).…”

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

“…The central and distal parts of the region between ZNF21 and DXS2SS have been especially difficult to clone in YACs in one study, with overall rates of 30% chimerism and 40-80% internal deletions (Boycott et al 1996). The only stable and reliable YACs for this region thus far are quite small (<200 kb) and were isolated either from an X chromosome-specific YAC library (Lee et al 1992) or from the St. Louis YAC library (Boycott et al 1996). In all, >100 different YACs were isolated from various YAC libraries without achieving overlapping clones across the entire region (Fisher et al 199S;Nelson et al 1995;Boycott et al 1996; this report).…”

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

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Long-range map of a 3.5-Mb region in Xp11.23-22 with a sequence-ready map from a 1.1-Mb gene-rich interval.

Schindelhauer

Hellebrand²,

Grimm

et al. 1996

Genome Res.

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Most of the yeast artificial chromosomes (YACs} isolated from the Xp11.23-22 region have shown instability and chimerism and are not a reliable resource for determining physical distances. We therefore constructed a long-range pulsed-field gel electrophoresis map that encompasses -3.5 Mb of genomic DNA between the loci TIMP and DXSI46 including a CpG-rich region around the WASP and TFE-3 gene loci. A combined YAC-cosmid contig was constructed along the genomic map and was used for fine-mapping of 15 polymorphic microsatellites and 30 expressed sequence tags (ESTs} or sequence transcribed sites {STSs}, revealing the following order: teI~SYN-TIMPHDXS426-ELKI~ZNF(CAJn

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Section: Toward a Cosmid Contig Connecting The Loci Dxsi03? And Dxs255mentioning

confidence: 99%

Section: Toward a Cosmid Contig Connecting The Loci Dxsi03? And Dxs255mentioning

confidence: 99%

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

Section: Yac Instability In a Gene-rich Regionmentioning

confidence: 99%

See 3 more Smart Citations

Long-range map of a 3.5-Mb region in Xp11.23-22 with a sequence-ready map from a 1.1-Mb gene-rich interval.

Schindelhauer

Hellebrand²,

Grimm

et al. 1996

Genome Res.

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Sequence-Based Exon Prediction around the Synaptophysin Locus Reveals a Gene-Rich Area Containing Novel Genes in Human Proximal Xp

et al. 1997

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The human Xp11.23-p11.22 interval has been implicated in several inherited diseases including Wiskott-Aldrich syndrome; three forms of X-linked hypercalciuric nephrolithiaisis; and the eye disorders retinitis pigmentosa 2, congenital stationary night blindness, and Aland Island eye disease. In constructing YAC contigs spanning Xp11. 23-p11.22, we have previously shown that the region around the synaptophysin (SYP) gene is refractory to cloning in YACs, but highly stable in cosmids. Preliminary analysis of the latter suggested that this might reflect a high density of coding sequences and we therefore undertook the complete sequencing of a SYP-containing cosmid. Sequence data were extensively analyzed using computer programs such as CENSOR (to mask repeats), BLAST (for homology searches), and GRAIL and GENE-ID (to predict exons). This revealed the presence of 29 putative exons, organized into three genes, in addition to the 7 exons of the complete SYP coding region, all mapping within a 44-kb interval. Two genes are novel, one (CACNA1F) showing high homology to alpha1 subunits of calcium channels, the other (LMO6) encoding a product with significant similarity to LIM-domain proteins. RT-PCR and Northern blot studies confirmed that these loci are indeed transcribed. The third locus is the previously described, but not previously localized, A4 differentiation-dependent gene. Given that the intron-exon boundaries predicted by the analysis are consistent with previous information where available, we have been able to suggest the genomic organization of the novel genes with some confidence. The region has an elevated GC content (>53%), and we identified CpG islands associated with the 5' ends of SYP, A4, and LMO6. The order of loci was Xpter-A4-LMO6-SYP-CACNA1F-Xcen, with intergenic distances ranging from approximately 300 bp to approximately 5 kb. The density of transcribed sequences in this area (>80%) is comparable to that found in the highly gene-rich chromosomal band Xq28. Further studies may aid our understanding of the long-range organization surrounding such gene-enriched regions.

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Construction of a 1.5-Mb Bacterial Artificial Chromosome Contig in Xp11.23, a Region of High Gene Content

Boycott

Zahorchak²,

Summer³

et al. 1998

Genomics

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A 2-Megabase Physical Contig Incorporating 43 DNA Markers on the Human X Chromosome at p11.23–p11.22 from ZNF21 to DXS255

Cited by 12 publications

References 0 publications

Long-range map of a 3.5-Mb region in Xp11.23-22 with a sequence-ready map from a 1.1-Mb gene-rich interval.

Long-range map of a 3.5-Mb region in Xp11.23-22 with a sequence-ready map from a 1.1-Mb gene-rich interval.

Sequence-Based Exon Prediction around the Synaptophysin Locus Reveals a Gene-Rich Area Containing Novel Genes in Human Proximal Xp

Construction of a 1.5-Mb Bacterial Artificial Chromosome Contig in Xp11.23, a Region of High Gene Content

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