A 7.5 Mb Sequence-Ready PAC Contig and Gene Expression Map of Human Chromosome 11p13–p14.1

Abstract

The region p13 of the short arm of human chromosome 11 has been studied intensely during the search for genes involved in the etiology of the Wilms' tumor, aniridia, genitourinary abnormalities, mental retardation (WAGR) syndrome, and related conditions. The gene map for this region is far from being complete, however, strengthening the need for additional gene identification efforts. We describe the extension of an existing contig map with P1-derived artificial chromosomes (PACs) to cover 7.5 Mb of 11p13-14.1. The extended sequence-ready contig was established by end probe walking and fingerprinting and consists of 201 PAC clones. Utilizing bins defined by overlapping PACs, we generated a detailed gene map containing 20 genes as well as 22 anonymous ESTs which have been identified by searching the RH databases. RH maps and our established gene map show global correlation, but the limits of resolution of the current RH panels are evident at this scale. Initial expression studies on the novel genes have been performed by Northern blot analyses. To extend these expression profiles, corresponding mouse cDNA clones were identified by database search and employed for Northern blot analyses and RNA in situ hybridizations to mouse embryo sections. Genomic sequencing of clones along a minimal tiling path through the contig is currently under way and will facilitate these expression studies by in silico gene identification approaches.

Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

“…Distal human chromosome 11p13 is well mapped and sequenced because of its involvement in the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation (WAGR) syndrome. It is moderately gene rich ( Craig and Bickmore, 1994 ; Fantes et al, 1995 ; Gawin et al, 1999 ) and contains both ubiquitously expressed genes and genes whose expression is tissue restricted ( Kent et al, 1997 ; Gawin et al, 1999 ; Kleinjan et al, 2002 ). There are also large (∼300 kb) intergenic stretches of DNA ( Kent et al, 1997 ; Gawin et al, 1999 ).…”

“…It is moderately gene rich ( Craig and Bickmore, 1994 ; Fantes et al, 1995 ; Gawin et al, 1999 ) and contains both ubiquitously expressed genes and genes whose expression is tissue restricted ( Kent et al, 1997 ; Gawin et al, 1999 ; Kleinjan et al, 2002 ). There are also large (∼300 kb) intergenic stretches of DNA ( Kent et al, 1997 ; Gawin et al, 1999 ). Gene order and spacing are conserved at the region of conserved synteny on mouse chromosome 2 (MMU2E) (P. Gautier, personal communication) ( http://www.ensembl.org/Mus_musculus/ ; http://www.ncbi.nlm.nih.gov/Omim/Homology/human11.html ).…”

PAX5-KIAA1549L: a novel fusion gene in a case of pediatric B-cell precursor acute lymphoblastic leukemia

“…As predicted by protein motif search, KIAA1549L harbors only a potential transmembrane domain encoded by exon 10, which, however, is not retained in the PAX5-KIAA1549L chimera. KIAA1549L is preferentially expressed in the human cerebral cortex and immunohistochemistry data suggest that KIAA1549L is localized in the nucleus as well as in cytoplasmatic vesicles [ 26 , 27 ].…”

Use of the Japanese Pufferfish (Fugu rubripes) in Comparative Genomics

“…Within this human region are a number of well-characterized genes (such as WT1, PAX6, and cleavage stimulation factor CSTF3), well-defined ones with little known about function (such as GA17 and reticulocalbin, RCN1), and poorly defined genes, only identified from expressed sequence tags (ESTs), partial transcripts, or predictions (such as TR2 and G2) (Gawin et al, 1999). The Fugu contig contains all these genes, in the same order and orientation, and by a combination of gene prediction and comparative sequence analysis, it was possible to define all the genes structurally (Fugu and human genes tend to share the same intron/exon structure).…”

“…Comparison of the human WAGR region on chromosome 11p13 and the syntenic region in the Fugu genome. The 2.2-Mb human region is covered by a series of BAC and cosmid clones (from Gawin et al, 1999), shown by the annotated lines above the human 11p region, which are being completely sequenced at the Sanger Centre, U.K. The approximate positions of the known genes are represented along the axis by the rectangular boxes.…”