Genetic Analysis of the Epidermal Differentiation Complex (EDC) on Human Chromosome 1q21: Chromosomal Orientation, New Markers, and a 6-Mb YAC Contig

The epidermal differentiation complex (EDC) unites a remarkable number of structurally, functionally, and evolutionarily related genes that play an important role in terminal differentiation of the human epidermis. It is localized within 2.05 Mb of region q21 on human chromosome 1. We have identified and characterized 24 yeast artificial chromosome (YAC) clones by mapping individual EDC genes, sequence-tagged site (STS) markers (D1S305, D1S442, D1S498, D1S1664), and 10 new region-specific probes (D1S3619–D1S3628). Here we present a contig that covers about 6 Mb of 1q21 including the entire EDC. Fluorescencein situhybridization on metaphase chromosomes with two YACs flanking the EDC determined its chromosomal orientation and established, in conjunction with physical mapping results, the following order of genes and STSs: 1cen–D1S442–D1S498–S100A10–THH–FLG–D1S1664–IVL–SPRR3–SPRR1–SPRR2–LOR–S100A9–S100A8–S100A7–S100A6–S100A5–S100A4–S100A3–S100A2–S100A1–D1S305–1qtel. These integrated physical, cytogenetic, and genetic mapping data will be useful for linkage analyses of diseases associated with region 1q21 and for the identification of novel genes and regulatory elements in the EDC.     

Chromosomal Assignment of the Interferon-Inducible Double-Stranded RNA-Dependent Protein Kinase (PRKR) to Human Chromosome 2p21-p22 and Mouse Chromosome 17 E2

The genes encoding P68 and P65 (PRKR), the human and mouse interferon-inducible dsRNA-dependent protein kinases, respectively, have been mapped to a single locus on human chromosome 2 (band p21) and on mouse chromosome 17 (band E2). These kinases have been implicated in the antiviral response mediated by interferon since their activation by virus-specific dsRNAs can lead to the inhibition of protein synthesis. Recently we have shown that the dsRNA-dependent kinase also may function as a tumor suppressor gene since defective mutant proteins induced malignant transformation. Identification of the chromosomal location of human PRKR permitted a survey of translocations, deletions, or other rearrangement events involving this segment of chromosome 2 in a variety of human malignancies. Finally, our results define a new region of conservation between the distal part of the short arm of chromosome 2 (band p21) and band E2 of mouse chromosome 17.     

The Genes Encoding the Human CC-Chemokine Receptors CC-CKR1 to CC-CKR5 (CMKBR1–CMKBR5) Are Clustered in the p21.3–p24 Region of Chromosome 3

The five human CC-chemokine receptors functionally characterized to date were mapped by using a radiation hybrid panel and YAC contigs. The genes encoding CC-CKR1, CC-CKR2, CC-CKR3, and CC-CKR5 (designated respectively CMKBR1, CMKBR2, CMKBR3, and CMKBR5 in the Genome Data Bank) were found to be clustered in the 3p21.3 region of chromosome 3, between the AFM362WB9 and the WI-6983 markers. The four genes fall within a total distance of about 350 kb. The fifth gene (CMKBR4, encoding the CC-CKR4 receptor) was located more distally (3p24) on the same chromosome, between the FB18G7 and the D3S1768 markers. These localizations were confirmed by mapping the genes into the YAC contigs covering these regions. The clustering of chemokine receptor genes suggests a relatively recent expansion of the gene family by gene duplication. Deletions and duplications of the 3p21 region have been described in neoplastic disorders of the hematopoietic lineage, suggesting a potential link with the CC-chemokine receptor gene family.     

A Sequence-Ready 840-kb PAC Contig Spanning the Candidate Tumor Suppressor Locus DBC1 on Human Chromosome 9q32–q33

A putative tumor suppressor locus involved in bladder cancer has been mapped to human chromosome 9q32–q33 and designated DBC1. Our previous microsatellite-based deletion mapping study indicated that DBC1 was localized between D9S1848 and AFMA239XA9. We have constructed an 840-kb sequence-ready contig composed of bacteriophage P1-derived artificial chromosomes (PACs), which encompasses DBC1. Clones were initially identified by screening a PAC library with markers localized to the region by physical mapping, and subsequently PAC end probes were used to complete the contig. This contig contains a minimum tiling path of six PAC clones between D9S1848 and AFMA239XA9. Three expressed sequence tags (ESTs) were mapped to the DBC1 region by screening 24 ESTs mapped to the surrounding area by radiation hybrids. One represented the gene for DBCCR1, a known candidate for DBC1, and the other two were novel. This contig and preliminary expression map form the basis for the identification of the bladder cancer tumor suppressor gene in this region.     

Mutations in PDX1, the Human Lipoyl-Containing Component X of the Pyruvate Dehydrogenase–Complex Gene on Chromosome 11p1, in Congenital Lactic Acidosis

We have identified and sequenced a cDNA that encodes an apparent human orthologue of a yeast protein-X component (ScPDX1) of pyruvate dehydrogenase multienzyme complexes. The new human cDNA that has been referred to as "HsPDX1" cDNA was cloned by use of the "database cloning" strategy and had a 1,506-bp open reading frame. The amino acid sequence of the protein encoded by the cDNA was 20% identical with that encoded by the yeast PDX1 gene and 40% identical with that encoded by the lipoate acetyltransferase component of the pyruvate dehydrogenase and included a lipoyl-bearing domain that is conserved in some dehydrogenase enzyme complexes. Northern blot analysis demonstrated that the major HsPDX1 mRNA was 2.5 kb in length and was expressed mainly in human skeletal and cardiac muscles but was also present, at low levels, in other tissues. FISH analysis performed with a P1-derived artificial chromosome (PAC)-containing HsPDX1 gene sublocalized the gene to 11p1.3. Molecular investigation of PDX1 deficiency in four patients with neonatal lactic acidemias revealed mutations 78del85 and 965del59 in a homozygous state, and one other patient had no PDX1 mRNA expression.     

A High-Resolution Genetic, Physical, and Comparative Gene Map of the Doublefoot (Dbf) Region of Mouse Chromosome 1 and the Region of Conserved Synteny on Human Chromosome 2q35

The mouse doublefoot (Dbf) mutant exhibits preaxial polydactyly in association with craniofacial defects. This mutation has previously been mapped to mouse chromosome 1. We have used a positional cloning strategy, coupled with a comparative sequencing approach using available human draft sequence, to identify putative candidates for the Dbf gene in the mouse and in homologous human region. We have constructed a high-resolution genetic map of the region, localizing the mutation to a 0. 4-cM (±0.0061) interval on mouse chromosome 1. Furthermore, we have constructed contiguous BAC/PAC clone maps across the mouse and human Dbf region. Using existing markers and additional sequence tagged sites, which we have generated, we have anchored the physical map to the genetic map. Through the comparative sequencing of these clones we have identified 35 genes within this interval, indicating that the region is gene-rich. From this we have identified several genes that are known to be differentially expressed in the developing mid-gestation mouse embryo, some in the developing embryonic limb buds. These genes include those encoding known developmental signaling molecules such as WNT proteins and IHH, and we provide evidence that these genes are candidates for the Dbf mutation.     

φX174 gene A protein does not cleave at a mouse mitochondrial DNA sequence homologous to the φX and G4 cleavage site

The light strand origin of replication of mouse mitochondrial DNA contains a 30-nucleotide region which is 60% homologous to the 30-nucleotide conserved sequence in φX174 and G4 viral DNAs known to contain the viral gene A protein cleavage site. Gene A protein does not cleave closed circular mouse mitochondrial DNA under conditions in which φX174 closed circular DNA is cleaved.     

A C-Terminal Helicase Domain of the Human Papillomavirus E1 Protein Binds E2 and the DNA Polymerase α-Primase p68 Subunit

The human papillomavirus (HPV) E1 and E2 proteins bind cooperatively to the viral origin of replication (ori), forming an E1-E2-ori complex that is essential for initiation of DNA replication. All other replication proteins, including DNA polymerase α-primase (polα-primase), are derived from the host cell. We have carried out a detailed analysis of the interactions of HPV type 16 (HPV-16) E1 with E2, ori, and the four polα-primase subunits. Deletion analysis showed that a C-terminal region of E1 (amino acids [aa] 432 to 583 or 617) is required for E2 binding. HPV-16 E1 was unable to bind the ori in the absence of E2, but the same C-terminal domain of E1 was sufficient to tether E1 to the ori via E2. Of the polα-primase subunits, only p68 bound E1, and binding was competitive with E2. The E1 region required (aa 397 to 583) was the same as that required for E2 binding but additionally contained 34 N-terminal residues. In confirmation of these differences, we found that a monoclonal antibody, mapping adjacent to the N-terminal junction of the p68-binding region, blocked E1-p68 but not E1-E2 binding. Sequence alignments and secondary-structure prediction for HPV-16 E1 and other superfamily 3 (SF3) viral helicases closely parallel the mapping data in suggesting that aa 439 to 623 constitute a discrete helicase domain. Assuming a common nucleoside triphosphate-binding fold, we have generated a structural model of this domain based on the X-ray structures of the hepatitis C virus and Bacillus stearothermophilus (SF2) helicases. The modelling closely matches the deletion analysis in suggesting that this region of E1 is indeed a structural domain, and our results suggest that it is multifunctional and critical to several stages of HPV DNA replication.     

The Tight Skin (Tsk) Mutation in the Mouse, a Model for Human Fibrotic Diseases, Is Tightly Linked to the β2-Microglobulin (B2m) Gene on Chromosome 2

The Tsk mutation in the mouse is characterized by the excessive accumulation of collagen in skin and various internal organs, including the heart and lungs. These connective tissue abnormalities are similar to those present in human systemic sclerosis or scleroderma. The Tsk mutation provides an opportunity to investigate, at the molecular level, the pathogenesis of tissue fibrosis. As a first step to cloning the Tsk gene, we report the localization of the Tsk mutation with respect to known molecular markers on mouse chromosome 2. N2 progeny carrying the Tsk mutation were obtained from an intersubspecific backcross of [(C57BL/6-pa +/+ Tsk × Mus castaneus)F1 × M. castaneus ] mice. Genomic DNA from each N2 mouse was subjected to Southern and PCR analyses to identify restriction fragment length polymorphisms and simple sequence length polymorphisms, respectively. Our results refine the location of Tsk to a 3-cM region, eliminate several genes from consideration as the Tsk mutation, identify molecular probes tightly linked with Tsk, and suggest candidate genes responsible for the Tsk phenotype.