Construction of a YAC contig spanning the Xq13.3 subband

doi:10.1016/0888-7543(95)80089-5

Genomics

Volume 26, Issue 1, 1 March 1995, Pages 115-122

https://doi.org/10.1016/0888-7543(95)80089-5 Get rights and content

Abstract

The loci involved in several X-linked mental retardation syndromes have been linked to the pericentromeric region of the X chromosome long arm (Xq12–q21). To isolate candidate genes for these diseases, we set up the construction of YAC contigs spanning this region. Two of these syndromes (the Juberg—Marsidi syndrome and the α-thalessemia mental retardation syndrome) have been recently linked, with high lod scores, to polymorphic probes previously assigned to Xq13.3. We therefore constructed a first YAC contig, encompassing this band, from DXS441 to PGK1. The physical map, deduced from the isolated clones, extends over 2.1 Mb of genomic DNA. Restriction analysis of the YAC contig allowed us to map precisely the loci previously assigned to that chromosomal region and to define their relative order. The validity of this physical map has been checked by comparing Sfi I digests of the YACs to genomic fragments obtained with the same enzyme. A cDNA selection approach, already performed with a previous partial contig, has been extended to cover the whole region.

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Transcript map of the human chromosome Xq11-Xq21 region: Localization of 33 novel genes and one pseudogene
1999, Gene
The human Xq11–Xq21.3 region has been implicated in several inherited disorders including dystonia-parkinsonism (DYT3), sideroblastic anemia and several specific and non-specific forms of mental retardation (MR) syndromes. As part of a positional cloning effort to identify MR genes, we have generated a YAC-based transcript map. We first constructed a YAC/STS framework by extending previously published contigs. This framework map consists of a minimal set of 119 clones, covering approximately 20 Megabases (Mb) and allowing the precise ordering of 71 STSs between DXS136 and DXS472. This YAC contig was then used to define the positions of genes and expressed sequence tags (ESTs) assigned to the Xcen–Xq21.3 region. In addition to the genes previously localized to this part of the X chromosome, 18 transcription units corresponding to additional known genes or gene family members, one pseudogene and 15 novel transcripts were mapped. This transcriptional map incorporates 51 transcription units and provides a useful resource of candidate genes for some of the disorders assigned to this region of the X chromosome.
A YAC contig in Xq22.3-q23, from DXS287 to DXS8088, spanning the brain- specific genes doublecortin (DCX) and PAK3
1998, Genomics
Although several genes for mental retardation and epilepsy, including double cortex/X-linked lissencephaly (DC/XLIS), have been localized to Xq21.3–q23, there has been no complete physical map of this region available. We constructed a YAC/STS contig map by initiating two yeast artificial chromosome (YAC) walks from the markers that flanked theDC/XLIScandidate gene region. We report an approximately 4-Mb contig extending fromDXS287toDXS8088,encompassingDXS1072andDXS1059,and composed of 52 YACs identified with 15 previously published STSs and 19 novel YAC-end STSs. This contig also contains two brain-specific genes,doublecortin(HGMW-approved symbolDCX), responsible forDC/XLIS,andPAK3,which may be responsible for neurological diseases localized to this region. The new contig extends and incorporates several previously published contigs, providing a total overlapping contig extending approximately 34 Mb fromDXS441in Xq13.1 toDXS8088in Xq23.
22-Mb integrated physical and genetic map based on YAC/STS content spanning the interval DXS1125-DXS95 in human Xq12-q21.31
1998, Gene
A YAC/STS map has been assembled spanning 22 Mb across Xq12–q21.31, between markers DXS1125 and DXS95. In addition to the landmark loci for the X-inactivation center XIST and the ATRX, ATP7A, phosphoglycerate kinase, POU3F4, and choroideremia genes, the candidate disease gene regions for torsion dystonia 3 and two X-linked mental retardation syndromes are included. Also, the human voltage-dependent anion channel gene (HVDAC1) has been placed near DXS986. The current map incorporates 211 YACs from five different libraries, formatted with 185 STSs that comprise 26 genetic linkage markers, 60 newly-developed YAC-end STSs, and eight ESTs. The multiple clone coverage and average resolution of one STS per 120 kb provide resources for disease gene searches and are facilitating complete sequencing of the region.
Determination of the genomic structure of the XNP/ATRX gene encoding a potential zinc finger helicase
1997, Genomics
The XNP/ATR-X gene is involved in several X-linked mental retardation phenotypes: the ATR-X syndrome, the Juberg–Marsidi syndrome, and some severe mental retardation phenotypes without α-thalassemia. Using a vectorette strategy, we have identified and sequenced the intron/exon boundaries of this gene. The gene is composed of 35 exons. It encodes a potential protein of 2492 amino acids. A search of the databases identified three zinc finger motifs within the 5′ end of the gene. Expression analysis in different tissues indicated that an alternative splicing event that involves exon 6 is occurring. One of these alternatively spliced transcripts is predominantly expressed in embryonic tissues. These data led us to search for mutations in the 5′ region in ATRX patients without other mutations in the 3′ region. In one patient a mutation was found in which part of exon 7 was removed from the XNP transcript, as a result of a mutation creating a novel splice site that is substituted for the natural splice site. This new splicing event removed one zinc finger motif. This is the first example of a mutation in XNP within the 5′ coding region. It suggests that mutations will be predominantly found in the helicase region as well as in the zinc finger regions and leads us to propose a large screening of additional patients.
Framework YAC contig anchored into a 3.2-Mb high-resolution physical map in proximal 11q13
1997, Genomics
Despite the presence on band q13 of chromosome 11 of a number of genes predisposing individuals to various human diseases, most of this genomic region remains loosely mapped. Moreover, there is a relative dearth of yeast artificial chromosome (YAC) contigs from genome-wide studies: YACs are irregularly distributed over this chromosomal region and have not been arranged into contigs. We have thus undertaken fine-scale mapping of a 3.2-Mb region flanked byACTN3andFGF3.Since this region has demonstrated a high degree of YAC instability, we have established a framework contig by anchoring YACs and cosmids into a high-resolution physical map based on fluorescencein situhybridization and long-range restriction mapping. The 3.2-Mb area studied includes the boundaries of regions thought to contain genes predisposing individuals to osteoporosis–pseudoglioma syndrome and insulin-dependent diabetes mellitus, as well as genes driving amplification events in human carcinomas. Another feature of this genomic area is that it cross-hybridizes to nonsyntenic regions of the genome. In addition, it spans the region where syntenic conservation with mouse chromosome 19 ends, making clones that we have anchored there valuable tools in understanding genome evolution.

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¹: Present address: Department of Genetics, Slovak Academy of Sciences, Vlarska 5, 83334 Bratislava, Slovakia.

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Construction of a YAC contig spanning the Xq13.3 subband

Abstract

Genomics

Genomics

Genomics

Genomics

Construction and characterization of a yeast artificial chromosome library containing seven haploid human genome equivalents

Proc. Natl. Acad. Sci. USA

The isochore organisation of the human genome

Annu. Rev. Genet.

Cloning of large segments of exogenous DNA into yeast by means of artificial chromosomes vectors

Science

Isolation of a candidate gene for Menkes disease that encodes a potential heavy metal binding protein

Nature Genet.

A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity

Anal. Biochem.

Physical and transcriptional mapping of DXS56-PGK1 1 Mb region: Identification of three new transcripts

Hum. Mol. Genet.

Cloning and expression of the murine homologue of a putative human X-linked nuclear protein gene closely linked to PGK1 in Xq13.3

Hum. Mol. Genet.

X-linked α-thalassemia/mental retardation (ATR-X) syndrome: Localization to Xq12–q21.31 by X inactivation and linkage analysis

Am. J. Hum. Genet.

Isolation of DNTR polymorphisms from yeast artificial chromosomes encompassing X chromosomal loci PGK1 and DXS56

Hum. Genet.