Identification of C15orf5, a heart-enriched transcript on chromosome 15q23-q24.

We have isolated C15orf5, a novel human gene lacking homology to any known protein. The C15orf5 gene encodes a transcript of 1,519 nt with an ORF of 94 amino acids and a predicted protein size of 11.5 kDa. Northern blot analysis showed enhanced expression of C15orf5 in heart. C15orf5 was mapped to chromosome 15q23-q24 using the Stanford TNG4 Radiation Hybrid panel.

PALML, a novel paralemmin-related gene mapping on human chromosome 1p21.

We describe PALML, a novel gene encoding a 551 amino acid protein with similarity to paralemmin and the paralemmin-like amino terminal domain of AKAP2, a protein kinase A anchor protein. PALML mRNA is expressed in many tissues and is most abundant in cardiac and skeletal muscle, while absent from brain and blood. Exogenously expressed PALML fusion protein has a widespread cytoplasmic localization, and it is excluded from the nucleus. Human PALML maps on human chromosome 1p21 (between D1S2767 and D1S223). SSCP-HD analysis of exonic sequences in patients with VUR (familial non-syndromic vesicoureteral reflux syndrome) excluded mutations in the PALML gene from causing this disease. PALML, paralemmin and AKAP2 share the presence of a conserved coiled coil region that may mediate protein interactions with shared partners. Based on its resemblance to paralemmin and AKAP2, PALML is hypothesized to be involved in regulating intracellular signaling and membrane-cytoskeletal interactions.

Identification and characterization of UBXD1, a novel UBX domain-containing gene on human chromosome 19p13, and its mouse ortholog.

We have identified a novel human gene, UBXD1, on chromosome 19p13, which encodes a putative protein containing a UBX domain. Expression analysis showed an enhanced presence in testis. We identified the corresponding orthologous genes in mouse and rat. The characterization of UBXD1 has allowed us to define a new class of UBX domain-containing proteins conserved during evolution.

Characterization of human FSD1, a novel brain specific gene on chromosome 19 with paralogy to 9q31.

We have characterized a novel human gene, FSD1, on chromosome 19. FSD1 has a BBC, FN3 and SPRY domain, it is distantly related to the midline 1 gene and is expressed only in the brain. We have established its exon-intron structure and we have identified the corresponding orthologous genes in other species. In addition, the identification of FSD1 has led us to identify a homologous counterpart sequence on chromosome 9.

PACSIN 3 is a novel SH3 domain cytoplasmic adapter protein of the pacsin-syndapin-FAP52 gene family.

Pacsins are cytoplasmic adapter proteins with an N-terminal FHC, a central coiled coil, and a C-terminal SH3 domain and several potential phosphorylation sites. Two murine Pacsin genes have been reported to date: Pacsin 1 (equivalent to rat Syndapin I), and Pacsin 2 (like rat Syndapin II and chicken focal adhesion protein FAP52). Rat syndapins have been well characterized as part of a synapse dynamin-associated protein complex involved in endocytosis and actin dynamics. Here we describe PACSIN 3, a third member of the pacsin gene family in humans and mice, which encodes a 424 amino acid cytoplasmic protein and has a ubiquitously expressed mRNA. Intracellular distribution was assessed by overexpression of exogenous tagged pacsin 3 protein. In addition, we report the cDNA sequence of human PACSIN 1, a gene encoding a 444 amino acid protein and its chromosome assignment to 6p21. PACSIN 1 mRNA is most abundant in brain, and is also present in heart, pancreas and liver. The close sequence conservation between the three pacsin gene products suggests they could be performing similar functions participating in the different tissues where these are expressed.

Identification and characterization of BTBD1, a novel BTB domain containing gene on human chromosome 15q24.

Working within the EUROIMAGE full-length cDNA sequencing project we have isolated BTBD1, a novel human gene with a BTB/POZ domain. This motif is found in developmentally regulated zinc finger proteins and in the kelch family of actin-associated proteins, and is thought to mediate protein-protein interactions. The BTBD1 gene encodes a transcript of 3188 nt with an ORF of 482 amino acids and a predicted protein product size of 52.7 kDa. Northern blot analysis revealed an enhanced BTBD1 expression in heart and skeletal muscle. We have identified a paralogous BTBD1 counterpart gene on chromosome 19, BTBD2. BTBD1 was mapped to chromosome 15q24. Conservation of multiple pairs of genes between 15q24 and 19p13.3-p12 suggests their possible common chromosomal origin. We show the existence of the murine BTBD1 and BTBD2 orthologous genes, as well as the partial rat and bovine homologs.

Cloning, mapping and expression analysis of C15orf4, a novel human gene with homology to the yeast mitochondrial ribosomal protein Ym130 gene.

We have identified C15orf4, a novel human gene showing homology to the yeast mitochondrial ribosomal protein YmL30. C15orf4 encodes a transcript of 1,006 nt with an ORF of 279 amino acids and a predicted protein size of 31.7 kDa. Expression of C15orf4 is enriched in testis. C15orf4 was positioned to chromosome 15q24 by radiation hybrid mapping. We have identified the C15orf4 mouse orthologue as well as homologues in other species.

Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-->q26 and 19p13.3-->p12.

As the result of the EUROIMAGE Consortium sequencing project, we have isolated and characterized a novel gene on chromosome 15, TM6SF1. It encodes a 370 amino acid product with enhanced expression in spleen, testis and peripheral blood leukocytes. We have identified another gene, paralogous to TM6SF1 on chromosome 19p12, TM6SF2, with an overall similarity of 68% and 52% identity at the protein level. This conservation has led us to uncover a series of eleven genes in 19p13.3-->p12 with close homology to genes in 15q24--> q26. The percentage of sequence similarity between each paralogous pair of genes at the protein level ranges between 43 and 89%. A partial conservation of synteny with mouse chromosomes 7, 8 and 9 is also observed. The corresponding orthologous genes in mouse of human TM6SF1 and TM6SF2 show a high degree of amino acid sequence conservation.

Identification and expression analysis of C3orf1, a novel human gene homologous to the Drosophila RP140-upstream gene.

We have isolated C3orf1, a novel gene on human chromosome 3 showing homology to the Drosophila RP140-upstream gene. When mutated, RP140-upstream causes lethality in flies through an unknown mechanism, perhaps by interfering with transcription of the RP140 RNA polymerase subunit. The human C3orf1 gene encodes a predicted membrane protein of 32.2 kDa with four transmembrane domains without any other known motifs. Northern blot analysis showed generalized expression of C3orf1, enhanced in heart and skeletal muscle. EST database searching revealed the existence of a homologue gene in mouse. Thus, the C3orf1 gene is conserved and may perform an essential function in all tissues in mammals.

Arrest of S-phase progression is impaired in Fanconi anemia cells.

Fanconi anemia (FA) is an inherited cancer-susceptibility disorder, characterized by genomic instability, hypersensitivity to DNA cross-linking agents, and a prolonged G2 phase of the cell cycle. We observed a marked dose-dependent accumulation of FA cells in the G2 compartment after treatment with 4,5',8-trimethylpsoralen (Me(3)Pso) in combination with 365 nm irradiation. Using bivariate DNA distribution methodology, we determined the proportion of replicating and arresting S-phase cells and observed that, whereas normal cells arrested DNA replication in the presence of Me(3)Pso cross-links and monoadducts, FA lymphoblasts failed to arrest DNA synthesis. Taken together, the above data suggest that, in response to damage induced by DNA cross-linking agents, the S-phase checkpoint is inefficient in FA cells. This would lead to accumulation of secondary lesions, such as single- and double-strand breaks and gaps. The prolonged time in G2 phase seen in FA cells therefore exists in order to allow the cells to remove lesions which accumulated during the preceding abnormal S phase.

Cloning, mapping and expression analysis of VPS33B, the human orthologue of rat Vps33b.

We have identified VPS33B, the human ortholog of rat Vps33b. VPS33B encodes a transcript of 2482 nt with an ORF of 617 amino acids and a predicted protein size of 70.6 kDa. VPS33B contains a Sec-1 domain shared with a family of proteins involved in protein sorting and vesicular trafficking. Enriched expression of VPS33B was observed in testis. VPS33B was positioned at chromosome 15q26.1 by radiation hybrid mapping.

Identification and expression analysis of C15orf3, a novel gene on chromosome 15q21.1-->q21.2.

We have isolated C15orf3, a novel human gene that lacks homology to any known gene family. The C15orf3 gene encodes a transcript of 1676 nt with an ORF of 187 amino acids and a predicted protein product size of 20.8 kDa. Northern blot analysis showed ubiquitous expression in adult tissues. EST database searching revealed the presence of C15orf3 homologs in rat and mouse. C15orf3 was mapped to chromosome 15q21.1-->q21.2 using the Stanford G3 radiation hybrid panel.

HMG20A and HMG20B map to human chromosomes 15q24 and 19p13.3 and constitute a distinct class of HMG-box genes with ubiquitous expression.

The HMG box encodes a conserved DNA binding domain found in many proteins and is involved in the regulation of transcription and chromatin conformation. We describe HMG20A and HMG20B, two novel human HMG box-containing genes, discovered within the EURO-IMAGE Consortium full-length cDNA sequencing initiative. The predicted proteins encoded by these two genes are 48.4% identical (73.9% within the HMG domain). The HMG domain of both HMG20 proteins is most similar to that of yeast NHP6A (38% to 42%). Outside of this domain, HMG20 proteins lack any significant homology to other known proteins. We determined the genomic structure and expression pattern of HMG20A and HMG20B. Both genes have several alternative transcripts, expressed almost ubiquitously. HMG20A maps to chromosome 15q24 (near D15S1227) and HMG20B to 19p13.3 (between D19S209 and D19S216). The HMG20 genes define a distinct class of mammalian HMG box genes.

Molecular spectra of HPRT deletion mutations in circulating T-lymphocytes in Fanconi anemia patients.

The principal cellular feature of Fanconi anemia (FA), an inherited cancer prone disorder, is a high level of chromosomal breakage, amplified after treatment with crosslinking agents. Three of the eight genes involved in FA have been cloned: FANCA, FANCC and FANCG. However, their biological functions remain unknown. We previously observed an excessive production of deletions at the HPRT locus in FA lymphoblasts belonging to the relatively rare complementation group D(1) and an increased frequency of glycophorin A (GPA) variants in erythrocytes derived from FA patients (2). In thi study, we examined the molecular nature of 31 HPRT mutations formed in vivo in circulating T-lymphocytes isolated from 9 FA male patients. The results show that in all FA patients investigated the deletions are by far the most prevalent mutational event in contrast to age matched healthy donors, in which point mutations predominate. The complementation group in the FA patients examined in the present study has not yet been defined. However, knowing that mutations in the FANCA and FANCC gene are found to be involved in at least 70% of the FA patients, it can be expected that the excessive production of deletions is a general feature of the FA phenotype. In addition, the spectrum of HPRT deletions observed in FA patients differs from that of healthy children: there is a high frequency of 3'-terminal deletions and a strikingly low proportion of V(D)J mediated events. Based on previous findings, a decreased fidelity of coding V(D)J joint formation (3) and an inaccurate repair of specific DNA double strand breaks via Non-Homologous End Joining (4), we propose that FA genes play a role in the control of the fidelity of rejoining of specific DNA ends. Such a defect may explain several basic features of FA, such as chromosomal instability and deletion pronenness.

Cloning, expression, and mapping of PDCD9, the human homolog of Gallus gallus pro-apoptotic protein p52.

We report the sequence, tissue distribution, and chromosome location of a novel gene, PDCD9 (programmed cell death 9). PDCD9 is the mammalian counterpart of the Gallus gallus pro-apoptotic protein p52. The human cDNA has an open reading frame of 1,314 nucleotides and was predicted to encode a protein of 438 amino acids with a calculated mass of 50 kDa. The protein sequences of chicken, mouse, and human PDCD9 are remarkably conserved. PDCD9 mRNA is expressed ubiquitously in adult tissues, displaying a stronger signal in heart, skeletal muscle, kidney, and liver. PDCD9 was mapped to chromosome 5q11.

Fanconi anemia C gene product plays a role in the fidelity of blunt DNA end-joining.

Mutations in genes controlling the correct functioning of the replicative, repair and recombination machineries may lead to genomic instability. A high level of spontaneous chromosomal aberrations amplified by treatment with DNA cross-linking agents is the hallmark of Fanconi anemia (FA), an inherited chromosomal instability syndrome associated with cancer proneness. Two of the eight FA genes have been cloned (FAA and FAC), but their function has not yet been defined. The lack of homology with known genes suggests the involvement of FA genes in a novel pathway specific to vertebrates. Using a DNA end-joining assay in cultured cells, we studied the processing of both blunt and cohesive-ended double strand breaks (DSB) in normal and FA cells. The results show that: (i) the overall ligation efficiency is normal in FA lymphoblasts; (ii) in FA-C, error-free processing of blunt-ended DSB is markedly decreased, resulting in a higher deletion frequency and larger deletion size; (iii) the fidelity of processing of blunt-DSB is completely restored in FACC cells (complemented with wild-type FAC gene) and the deletion size shifted to values similar to that observed in normal cells; (iv) the fidelity of cohesive end-joining is not affected in FA cells; (v) activities and/or expression of known factors involved in DSB processing, such as the components of the DNA-PK complex and XRCC4, are normal in FA cells. Our results provide strong evidence that the lack of a functional FAC gene results in loss of fidelity of end-joining, which likely accounts for the FA-C phenotype of chromosome instability. We conclude that FAC, and perhaps all FA gene products, are likely to play a role in the fidelity of end-joining of specific DSB.

The fidelity of double strand breaks processing is impaired in complementation groups B and D of Fanconi anemia, a genetic instability syndrome.

In mammalian cells, nonhomologous end-joining is the predominant mechanism to eliminate DNA double strand breaks. Such events are at the origin of deletion mutagenesis and chromosomal rearrangements. The hallmark of Fanconi anemia, an inherited cancer prone disorder, is increased chromosomal breakage associated to over-production of deletions. Knowing that double strand breaks are at the origin of deletion mutagenesis, the question arises whether their processing is affected in FA. We set up a "host cell end-joining assay" to analyze the fate of double strand breaks into extrachromosomal substrates transiently replicated in normal and FA-D lymphoblasts. Although no difference in plasmid survival was found, blunt-ended breaks were sealed with significantly lower fidelity in FA cells, resulting in a higher deletion frequency and a larger deletion size. The results suggest that FA-D and FA-B gene products are likely to play a role in end-joining fidelity of specific DNA double strand breaks.

Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation.

DNA polymerase II (Pol II) is regulated as part of the SOS response to DNA damage in Escherichia coli. We examined the participation of Pol II in the response to oxidative damage, adaptive mutation, and recombination. Cells lacking Pol II activity (polB delta 1 mutants) exhibited 5- to 10-fold-greater sensitivity to mode 1 killing by H2O2 compared with isogenic polB+ cells. Survival decreased by about 15-fold when polB mutants containing defective superoxide dismutase genes, sodA and sodB, were compared with polB+ sodA sodB mutants. Resistance to peroxide killing was restored following P1 transduction of polB cells to polB+ or by conjugation of polB cells with an F' plasmid carrying a copy of polB+. The rate at which Lac+ mutations arose in Lac- cells subjected to selection for lactose utilization, a phenomenon known as adaptive mutation, was increased threefold in polB backgrounds and returned to wild-type rates when polB cells were transduced to polB+. Following multiple passages of polB cells or prolonged starvation, a progressive loss of sensitivity to killing by peroxide was observed, suggesting that second-site suppressor mutations may be occurring with relatively high frequencies. The presence of suppressor mutations may account for the apparent lack of a mutant phenotype in earlier studies. A well-established polB strain, a dinA Mu d(Apr lac) fusion (GW1010), exhibited wild-type (Pol II+) sensitivity to killing by peroxide, consistent with the accumulation of second-site suppressor mutations. A high titer anti-Pol II polyclonal antibody was used to screen for the presence of Pol II in other bacteria and in the yeast Saccharomyces cerevisiae. Cross-reacting material was found in all gram-negative strains tested but was not detected in gram-positive strains or in S. cerevisiae. Induction of Pol II by nalidixic acid was observed in E. coli K-12, B, and C, in Shigella flexneri, and in Salmonella typhimurium.

Detection of hepatitis B virus DNA in human serum samples: use of digoxigenin-labeled oligonucleotides as modified primers for the polymerase chain reaction.

Nonradioactive techniques have been used for the direct detection of hepatitis B virus DNA in human serum samples. A comparison of two different systems using digoxigenin-labeled DNA probes is presented. Furthermore, oligonucleotides containing one molecule of the hapten digoxigenin at the 5'-end were prepared and used as primers for the polymerase chain reaction. Amplified DNA can be directly analyzed with anti-digoxigenin Fab fragments labeled with alkaline phosphatase and chemiluminescent substrates.