Isolation and mapping of human T-cell protein tyrosine phosphatase sequences: Localization of genes and pseudogenes discriminated using fluorescence hybridization with genomic versus cDNA probes

Journal Article · Tue Jun 01 04:00:00 EDT 1993 · Genomics; (United States)

DOI:https://doi.org/10.1006/geno.1993.1239· OSTI ID:7077025

Johnson, C V; Lawrence, J B ^[1]; Cool, D E; Glaccum, M B; Fischer, E H ^[2]; Green, N; Hill, D E ^[3]; Bruskin, A ^[4]

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1. Univ. of Massachusetts Medical Center, Worcester, MA (United States)
2. Univ. of Washington, Seattle (United States)
3. Applied BioTechnology, Cambridge, MA (United States)
4. Applied BioTechnology, Cambridge, MA (United States) Oncogene Science Inc., Uniondale, NY (United States)

This work reports the isolation, partial characterization, and chromosomal mapping of several human T-cell protein tyrosine phosphatase (PTPase) sequences and provides a direct comparison of the specificity of cDNA versus genomic probes in discriminating the location of genes versus pseudogenes by fluorescence in situ hybridization. In initial attempts to map the T-cell (TC) PTP gene using a 2-kb cDNA, several labeled sites were noted, raising the possibility of multiple related sequences within the genome. To address this, four genomic clones were obtained with homology to the TC PTP cDNA and characterized for their primary structure and their position within the human genome. Based on the presence or absence of an open reading frame and the intron/exon structure, two of these clones were found to be overlapping sequences encoding the true TC PTP gene and two were highly related but distinct processed pseudogenes. The TC PTP gene (gene symbol PTPN2) encoded by clones L17-2 and L5-1 localized to chromosome 18q11.2-q11.3, whereas pseudogenes encoded by clones L17-1, entitled TCPS1 (gene symbol PTPN2P1), and clone L18, entitled TCPS13 (gene symbol PTPN2P2), mapped to chromosomes 1q22-q24 and 13q12-q13, respectively. A direct comparison of the specificity of genomic and cDNA probes demonstrated that under identical conditions the genomic probes (containing both exon and intron sequences) readily identified a single specific site of hybridization, whereas the cDNA identified sites of both the gene and its pseudogenes. While providing mapping and sequencing information of the TC PTPase sequences, this work illustrates a strategy for addressing a recurrent problem in gene mapping studies where highly related sequences exist within the genome. 32 refs., 4 figs. 1 tab.

• OSTI ID: 7077025
• Journal Information: Genomics; (United States), Journal Name: Genomics; (United States) Vol. 16:3; ISSN GNMCEP; ISSN 0888-7543
• Country of Publication: United States
• Language: English

Related Subjects

550400* -- Genetics
59 BASIC BIOLOGICAL SCIENCES
ANIMAL CELLS
BIOLOGICAL MATERIALS
BLOOD
BLOOD CELLS
BODY FLUIDS
CHROMOSOMES
CLONING
CONNECTIVE TISSUE CELLS
DNA HYBRIDIZATION
DNA SEQUENCING
DNA-CLONING
ENZYMES
ESTERASES
GENES
GENETIC MAPPING
HUMAN CHROMOSOME 1
HUMAN CHROMOSOME 13
HUMAN CHROMOSOME 18
HUMAN CHROMOSOMES
HYBRIDIZATION
HYDROLASES
LEUKOCYTES
LYMPHOCYTES
MAPPING
MATERIALS
ORGANIC COMPOUNDS
PHOSPHATASES
PROTEINS
SOMATIC CELLS
STRUCTURAL CHEMICAL ANALYSIS