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Identification of CXorf1, a novel intronless gene in Xq27.3, expressed in human hippocampus.

We have identified and characterized a novel human gene (Nomenclature Committee of the Genome Database GDB-assigned symbol CXorf1) that maps to the long arm of the X chromosome in Xq27 between loci DXS369 and DXS181, approximately 2.5 Mb centromeric to the FMR1 gene. The CXorf1 gene is conserved in primates, cow, and horse but not in mouse and rat. Northern blot analysis revealed two transcripts, present in the brain and in the G361 melanoma cell line. In situ hybridization experiments performed on sections of human hippocampus showed a clear, uneven localization of the CXorf1 mRNA in specific subfields of this brain area. In particular, CXorf1 was localized in the granular-cell layer of the dentate gyrus and in the CA2-CA3 subfields of Ammon's horn. CXorf1 is one of the first genes from this region to be characterized in detail and, on the basis of its chromosomal location and expression pattern, may have an important function in the brain.

Amino Acid Sequence↗

The human TREM gene cluster at 6p21.1 encodes both activating and inhibitory single IgV domain receptors and includes NKp44.

We have characterized a cluster of single immunoglobulin variable (IgV) domain receptors centromeric of the major histocompatibility complex (MHC) on human chromosome 6. In addition to triggering receptor expressed on myeloid cells (TREM)-1 and TREM2, the cluster contains NKp44, a triggering receptor whose expression is limited to NK cells. We identified three new related genes and two gene fragments within a cluster of approximately 200 kb. Two of the three new genes lack charged residues in their transmembrane domain tails. Further, one of the genes contains two potential immunotyrosine Inhibitory motifs in its cytoplasmic tail, suggesting that it delivers inhibitory signals. The human and mouse TREM clusters appear to have diverged such that there are unique sequences in each species. Finally, each gene in the TREM cluster was expressed in a different range of cell types.

Amino Acid Motifs↗

Comparative genome organization of human, murine, and feline MHC class II region.

To study comparative molecular dynamics in the genesis of the major histocompatibility complex (MHC), we determined a complete nucleotide sequence spanning 758,291 bp of the domestic cat (Felis catus) extended and classical class II region. The feline class II MHC includes 44 genes (31 predicted to be expressed) which display DNA sequence homology and ordered gene synteny with human HLA and mouse H2, in extended class II and centromere proximal regions (DM to DO) of the classical class II region. However, remarkable genomic alterations including gene gain and loss plus size differentials of 250 kb are evident in comparisons of the cat class II with those of human and mouse. The cat MHC lacks the entire DQ region and retains only relict pseudogene homologs of DP genes, compensated by expansion and reorganization of seven modern DR genes. Repetitive gene families within the feline MHC comprise 35% of the feline MHC with very different density and abundance of GC levels, SINES, LINES, STRs, and retro-elements from the same repeats in human and mouse MHC. Comparison of the feline MHC with the murine and human MHC offers a detailed view of the consequences of genome organization in three mammalian lineages.

Animals↗

A gene recently inactivated in human defines a new olfactory receptor family in mammals.

The olfactory receptor (OR) gene family constitutes one of the largest multigene families and is distributed among many chromosomal sites in the human genome. Four OR families have been defined in mammals. We previously demonstrated that a high fraction of human OR sequences have incurred deleterious mutations, thus reducing the repertoire of functional OR genes. In this study, we have characterized a new OR gene, 912-93, in primates. This gene is unique and it defines a new OR family. It localizes to human chromosome 11q11-12 and at syntenical sites in other hominoids. The sequence marks a previously unrecognized rearrangement of pericentromeric material from chromosome 11 to the centromeric region of gibbon chromosome 5. The human gene contains a nonsense point mutation in the region corresponding to the extracellular N-terminus of the receptor. This mutation is present in humans of various ethnic groups, but is absent in apes, suggesting that it probably appeared during the divergence of humans from other apes, <4 000 000-5 000 000 years ago. A second mutation, a frameshift at a different location, has occurred in the gorilla copy of this gene. These observations suggest that OR 912-93 has been recently silenced in human and gorilla, adding to a pool of OR pseudogenes whose growth may parallel a reduction in the sense of smell in primates.

Amino Acid Sequence↗

[Karyological study of some Corvine birds (Corvidae, aves)].

Karyotypes were studied in the hooded and carrion crows, their naturally occurred hybrids, the jungle crow, the azure-winged magpie (2n = 80 in all aforementioned birds), and the magpie (2n = 82). Corvine birds of Primorskii Krai were karyotyped for the first time. In addition to the similarity in the diploid chromosome sets, corvine birds were shown to have a similar structure of karyotype: in all studied birds, 14 macrochromosomes (Mchs) classified into three groups according to their size were detected. By karyotype structure, birds belonging to the same genus are similar. Some intergeneric differences are due to a change in the position of centromeres of the largest and sex chromosomes. Karyotypes of interspecific hybrids of crows are remarkable for the presence of heteromorphic (t/st) chromosome pair 2 in some individuals, which apparently does not affect their fecundity. Using differential C-banding, the sex chromosome W in female magpies was identified. In addition, heteromorphism was detected in C-bands of homologs of Mch pair 4 in the hooded crow. In the jungle crow, the azure-winged magpie, and the magpie, bright QH-bands and numerous G-bands were detected on Mchs and on some microchromosomes only. Active Ag-NOR-bands were detected on one macrochromosome pair in the magpie. In all, the karyotype structure of corvine birds is comparable to the basic structural scheme of the karyotype in the order Passeriformes, which confirms the concept of conservatism of the avian karyotype.

Animals↗

Conservation of heterochromatin protein 1 function.

Heterochromatin represents a cytologically visible state of heritable gene repression. In the yeast, Schizosaccharomyces pombe, the swi6 gene encodes a heterochromatin protein 1 (HP1)-like chromodomain protein that localizes to heterochromatin domains, including the centromeres, telomeres, and the donor mating-type loci, and is involved in silencing at these loci. We identify here the functional domains of swi6p and demonstrate that the chromodomain from a mammalian HP1-like protein, M31, can functionally replace that of swi6p, showing that chromodomain function is conserved from yeasts to humans. Site-directed mutagenesis, based on a modeled three-dimensional structure of the swi6p chromodomain, shows that the hydrophobic amino acids which lie in the core of the structure are critical for biological function. Gel filtration, gel overlay experiments, and mass spectroscopy show that HP1 proteins can self-associate, and we suggest that it is as oligomers that HP1 proteins are incorporated into heterochromatin complexes that silence gene activity.

Amino Acid Sequence↗

A clade of New World primates with distinctive alphoid satellite DNAs.

Centromerically located alphoid satellite DNAs are present in all primates. They typically consist of arrays of a 340-bp monomeric unit that is composed of related, but diverged, 170-bp subunits. A unique monomeric unit has recently been described: the alphoid satellite monomers of the neotropical primate Chiropotes satanas (bearded saki) are typically 539 bp in length. In addition, a number of smaller satellite sequences are present in this species. Analysis of two primates closely related to Chiropotes, Pithecia irrorata (saki) and Cacajao melanocephalus (uakari), show that they also contain unique alphoid satellites that are different from those of Chiropotes and different from one another. Southern blot and sequence analyses suggest that an alphoid satellite rearrangement(s) occurred early in the history of the tribe Pitheciini (Chiropotes, Pithecia, Cacajao) and that rearrangements are continuing to occur in this group of primates.

Animals↗

Responder (Rsp) alleles in the segregation distorter (SD) system of meiotic drive in Drosophila may represent a complex family of satellite repeat sequences.

In D. melanogaster males carrying Segregation Distorter (SD) second chromosomes, sperm receiving sensitive alleles of the Responder (Rsp) locus are subject to high rates of dysfunction. The Rsp region is located in 2R immediately adjacent to the centromere in heterochromatic band 39, and covers roughly 600 kb of material, of which approximately 85 kb is comprised of several hundred copies of a 240-bp satellite DNA sequence. Cytological observations as well as molecular analysis of rearrangements which bisect h39 indicate that sensitivity of the Rsp target to SD action is also subdivisible, and sensitivities of the component pieces appear to be correlated with copy number of the 240 bp repeat. In an attempt to examine possible higher order sequence structure for these blocks, PCR using single primers derived from a canonical repeat was used to identify potential reversals of direction of tandem arrays; that is, head-to-head or tail-to-tail junctions. Surprisingly, for two different Rsp alleles, only a single such reversal product for each was identified, differing in size and sequence between alleles. Sequencing of PCR products identified diverged copies of the canonical repeats that would not have been found using the levels of DNA stringency employed in earlier studies. Examination of Southern digests and slot-blots for DNA quantification indicates that adding the estimated numbers of such diverged copies to the canonical repeat copies discovered earlier is potentially sufficient to account for the entire 600 kb Rsp region. This adds strength to the hypothesis that this extended family of repeats is in fact the target of SD-mediated sperm dysfunction. Implications of these results for understanding the evolution of repetitive DNA are also discussed.

Animals↗

Construction of a bovine chromosome 19 linkage map with an interspecies hybrid backcross.

Interspecific hybrid backcross animals from a Bos taurus x Bos gaurus F1 female were used to construct a linkage map of bovine Chromosome (Chr) 19. This map includes eight previously unmapped type I anchor loci, CHRNB1, CRYB1, GH1, MYL4, NF1, P4HB, THRA1, TP53, and five microsatellite markers, HEL10, BP20, MAP2C, ETH3, BMC1013, from existing linkage maps. The linkage relationship was determined to be centromere-HEL10-18.8cM-NF1-4.0cM-CRYB1-11 .2cM-(BP20, CHRNB1, TP53)-4.0cM-(MAP2C, GH1, MYL4, THRA1)-14.4cM-P4HB-11.2cM-ETH3-4. 0cM-BMC1013. It was previously revealed that bovine Chr 19 contains the largest known conserved autosomal synteny among human, bovine, and mouse. This study has shown that gene orders within this segment are not conserved among the three species. We propose structural changes in an ancestral mammalian chromosome to account for these differences. This is the first interspecific hybrid backcross used in bovine linkage studies, and it has proven to be an effective tool for incorporating bovine type I loci into the linkage map even with the small sample size presently available. This resource will facilitate the generation of comparative linkage maps that address gene order and effectively predict the locations of unmapped loci across species.

Animals↗

Case study: periodic follow-up is necessary in morphea profunda to identify systemic evolution.

The term "morphea" includes a wide spectrum of clinical entities, varying from localized plaques of only cosmetic importance to deep lesions resulting in considerable morbidity for the patient. In fact, although survival rates are no different from that of the general population, localized scleroderma may be associated with development of substantial disability, as occurs in deep morphea and in pediatric patients (disabling pansclerotic morphea of children). We report a case of morphea profunda affecting a young man with severe, rapidly progressive, widespread skin involvement and focus on the eventual systemic evolution of such cases. A 40-year-old man was admitted in 2002 for progressive subcutaneous indurations, preferentially involving the right side of the trunk. His health was altogether good, with the exception of a beginning chronic obstructive bronchopneumopathy. There was no family or personal history of dysmetabolic, cardiovascular, neoplastic, or cutaneous disease. Three years earlier, the patient had noted the appearance of two infiltrated, intensely red lesions on the right laterocervical and paraumbilical regions. These had been interpreted as subcutaneous lipomatosis on the basis of an ultrasound scan. The lesions had become progressively larger, while their surface had assumed a scleroatrophic appearance. Thereafter, other lesions had developed on his chest and lower limbs, mostly distributed on the right side of the body. Clinical examination revealed well demarcated, depressed sclerotic plaques with ivory-colored centers and erythematous borders ("lilac ring") localized on the neck, chest, and lower abdomen and limbs (Figure 1). They were bound to the deeper structures and arranged in a band-like linear distribution on the right side of the chest and abdomen where they extended horizontally for more than 10 cm in diameter. These lesions were totally asymptomatic. In addition, arborizing telangiectasias were evident on the neck and upper chest (Figure 2). Laboratory investigations provided normal range of erythrocyte sedimentation rat and C reactive protein levels and other inflammation markers. Antinuclear antibody, antidouble-strand DNA, antimitochondrial, anti-extractable antigens (anti-centromere, anti-Scl-70, anti-U1RNP), and anti-Borrelia burgdorferi antibodies were negative. Circulating immunocomplexes binding C1q were substantially increased. Oesophageal x-rays and lower limb electromyography were within normal limits; ventilatory function testing revealed a mild obstruction consistent with the beginning of chronic obstructive pulmonary disease. Although nailfold capillaroscopy documented nonspecific findings of connective tissue disease (mega-capillaries, segmentary dilatation and destruction), the laser-Doppler flussimetry revealed few signs of microcirculatory abnormalities, in absence of Raynaud's phenomenon. An abdominal wall ultrasonography, performed on a sclerotic plaque, documented thinning of the subcutaneous tissue, with increase of the fibrous component and lower fascia and muscle retraction. The biopsy specimen from the abdominal region included fascia and the subcutaneous tissue (previously obtained from the lower abdomen) with epidermal atrophy, a thickening and homogenization of collagen bundles in the deep dermis and hair reduction. A perivascular lympho-monocytic and plasmacellular infiltration with a dermo-epidermal distribution was present. Moreover, septal fibrosis with a perivascular lymphoplasmacellular inflammatory infiltrate was documented within the abdominal rectus muscle. The diagnosis of morphea profunda was made on the basis of clinical and histopathological findings. A therapeutic regimen based on amino benzoic potassium (Potaba; Glenwood, LLC, Glenwood, NJ), oral prednisone, and topical clobetasol was started. After several months of follow-up, the patient had obtained only moderate improvement of the clinical findings.

Adult↗

Fitness reduction associated with the deletion of a satellite DNA array.

Satellite DNA refers to a class of tandem repeats of very simple sequences, usually A + T or G + C rich, which form a satellite band on a CsCl gradient. Their ubiquity and abundance in higher eukaryotes have led to speculation about their functions. It has often been suggested that satellite DNAs are merely innocuous genetic parasites or comprise 'junk' DNA. The recent identification of an array of satellite DNA repeats as the Responder (Rsp) locus of Drosophila melanogaster provides a new perspective on these elements. Rsp is in the centromeric heterochromatin of most natural second chromosomes. It causes spermatids bearing it to degenerate after meiosis when the homologous second chromosome is a Segregation Distorter (SD) chromosome. That is, SD targets the Rsp locus on its homologue for destruction during spermatogenesis, causing meiotic drive. Why then does the Rsp locus, a large array of satellite repeats, exist at all? One plausible explanation is that its existence contributes to the fitness of flies bearing it, compensating for the loss through meiotic drive. A direct demonstration of the usefulness of any family of satellite DNA is to compare the fitnesses of individuals with and without it. Previously, such an experiment has been difficult because the absence of a characteristic phenotype has precluded an efficient selection of deletion mutations. In this report we attempt to demonstrate a fitness reduction associated with the deletion of Rsp satellite DNA as well as the life stages at which such a reduction occurs.

Animals↗

Patients with anticentromere antibodies, clinical features, diagnoses and evolution.

The sera of 1373 patients derived from a random population of 2627 individuals examined in a rheumatology outpatient clinic were found to be positive for antinuclear antibodies (ANA). Forty-seven of 1373 ANA positive patients (3.42%) presented a pattern of anticentromere antibodies (ACA), and of these 41 were followed-up. The predominant clinical features among ACA positive patients were Raynaud's phenomenon, arthralgias, scleroderma affecting the hands, feet, face and forearms, telangiectases and pulmonary involvement. There were 26 patients (64%) with limited cutaneous systemic sclerosis (lSSc), seven with primary Sjögren's syndrome (Ss) (17%), five with idiopathic Raynaud's phenomenon (IRPh) (12%) and three (7%) with other diseases. The lSSc subset was characterized by a significantly younger age for disease onset than for the IRPh patients. The Raynaud's phenomenon of lSSc patients lasted for many years before the onset of scleroderma, while their pulmonary involvement was mild and subclinical. The Ss patients with ACA were characterized by a lower incidence of parotid gland enlargement and anti-La (SSB) antibodies than described in the literature. Finally, the presence of ACA correlates with the clinical criteria proposed for the diagnosis of lSSc.

Adult↗

Variation of C-bands in the chromosomes of several subspecies of Rattus rattus.

All subspecies of black rats (Rattus rattus) used in the present study are characterized by having large and clear C-bands at the centromeric region. The appearance of the bands, however, is different in the subspecies. Chromosome pair No. 1 in Asian type black rats (2n=42), which are characterized by an acrocentric and subtelocentric polymorphism, showed C-band polymorphism. In Phillipine rats (R. rattus mindanensis) the pair was subtelocentric with C-bands, but in Malayan black rats (R. rattus diardii) it was usually acrocentric with C-bands. In Hong-Kong (R. rattus flavipectus) and Japanese black rats (R. rattus tanezumi) it was polymorphic with respect to the presence of acrocentrics with C-bands or subtelocentrics without C-bands. The other chromosomes pairs showed clear C-bands, but in Hong-Kong black rats the pairs No. 2 and 5 were polymorphic with and without C-bands. In Japanese black rats, 6 chromosome pairs (No. 3, 4, 7, 9, 11 and 13) were polymorphic in regard to presence and absence of C-bands, but the other 5 chromosome pairs (No. 2, 5, 6, 8 and 10) showed always absence of C-bands. Only pair No. 12 usually showed C-bands. C-bands in small metacentric pairs (No. 14 to 20) in Asian type black rats generally large in size, but those in the Oceanian (2n=38) and Ceylon type black rats (2n=40) were small. In the hybrids between Asian and Oceanian type rats, heteromorphic C-bands, one large and the other small, were observed. Based on the consideration of karyotype evolution in the black rats, the C-band is suggested to have a tendency toward the diminution as far as the related species are concerned.

Animals↗

A transcription map of the major histocompatibility complex (MHC) class I region.

We have applied cDNA hybridization selection to nine YACs spanning 3 Mb of genomic DNA from a region centromeric to HLA-A to the histone cluster that lies telomeric to the human major histocompatibility complex (MHC). In addition to Class I genes and pseudogenes, we describe over 63 genes and 23 additional expressed sequence tags distributed throughout the region. Many of the full-length genes belong to gene families. Prominent among these are a group of genes encoding proteins showing homology to the carboxyl-terminal sequences of butyrophilin and an additional group of zinc finger genes. We also detected several previously undefined genes that are specifically expressed in cells of the immune system, indicating a more complex role of the MHC in the immune response than has been appreciated.

Amino Acid Sequence↗

Sequence and chromosomal localization of mouse annexin XI.

Mouse annexin XI (anx11)2 was cloned from a macrophage cDNA library and characterized by genetic linkage mapping, DNA sequencing, and structural comparison with other annexins. The Anx11 gene localized to mouse chromosome 14 in close linkage with the Rarb, Plau, and Wnt5a genes near the centromere and 1.8 cM distal from the Anx7 gene. The open reading frame was flanked by long, untranslated regions and encoded a 503-amino-acid protein with 93.1% identity to its human orthologue. Its 189-aa amino terminus corresponded to the widely expressed variant 1 of two possible, alternatively spliced forms. A previously described peptide from Aplysia brasiliana was identified as a closely related invertebrate homologue. Since annexin XI is known to be localized in the nucleus at certain stages of development, the identification of a region in tetrad repeats 3 and 4 resembling the "chromo box" domain may be relevant to a nuclear regulatory function of annexin XI. Knowledge of the mouse cDNA sequence and genetic map location will assist in the analysis of genomic organization and expression and provide a useful animal model to investigate gene function and hereditary phenotype for annexin XI.

Amino Acid Sequence↗

[The clinical spectrum of patients with anticentromere antibodies].

In order to define the clinical associations and diagnostic meaning of anticentromere antibodies in a random population of patients, clinical and serological findings were studied with the evolution of 16 patients selected only because of their positiveness to anticentromere antibodies, detected by indirect immunofluorescence on HEp-2 cells and confirmed in chromosome spreads of HMcB cells. The most frequent diagnosis was systemic sclerosis in 9 patients (56%) especially in its variety Limited Cutaneous Systemic Sclerosis/CREST (7 patients). The rest of the cases (44%) showed different diseases (3 isolated Raynaud's phenomena, 1 Sjögren's syndrome, 1 seronegative polyarthritis, 1 undifferentiated connective tissue disease and a probable sarcoidosis). Therefore, even tough the more frequent clinical entity associated to anticentromere antibodies was systemic sclerosis and especially its variety Limited Cutaneous Systemic Sclerosis/CREST its diagnostic specificity is relatively low. The most frequent clinical association in our group of patients with positive anticentromere antibodies has been Raynaud's phenomena, alone or associated to other processes, being found in all but one of the studied patients (94%).

Antibodies, Antinuclear↗

A human homologue of the Drosophila tumour suppressor gene l(2)gl maps to 17p11.2-12 and codes for a cytoskeletal protein that associates with nonmuscle myosin II heavy chain.

Inactivation of the tumour suppressor gene lethal(2) giant larvae (D-lgl) of Drosophila leads to malignant transformation of the presumptive adult optic centers in the larval brain and tumours of the imaginal discs. These malignancies result from the disorganization of a cytoskeletal network in which the D-LGL protein participates. Here we describe the isolation of a cDNA encoding the human homologue to the D-lgl gene designated as hugl. The hugl cDNA detects a locus spanning at least 25 kilobases (kb) in human chromosome band 17p11.2-12, which is centromeric to the p53 gene and recognizes a 4.5 kb RNA transcript. The hugl gene is expressed in brain, kidney and muscle but is barely seen in heart and placenta. Sequence analysis of the hugl cDNA demonstrates a long open reading frame, which has the potential to encode a protein of 1057 amino acids with a predicted molecular weight of 115 kDaltons (kD). To further substantiate and identify the HUGL protein, we have prepared polyclonal rabbit antibodies against synthetic peptides corresponding to the amino and carboxyl termini of the conceptual translation product of the hugl gene. The affinity-purified anti-HUGL antibodies recognize a single protein with an apparent molecular weight of approximately 115 kD. Similar to the Drosophila protein, HUGL is part of a cytoskeletal network and, is associated with nonmuscle myosin II heavy chain and a kinase that specifically phosphorylates HUGL at serine residues.

Amino Acid Sequence↗

Identification and characterization of LASP2 gene in silico.

LASP1 (also known as MLN50) gene, located centromeric to the PPP1R1B-ERBB2-GRB7 locus on human chromosome 17q12, is amplified and over-expressed in breast cancer. Here, we identified and characterized a novel LASP1-related gene, LASP2, by using bioinformatics. Nucleotide sequence of human LASP2 cDNA was determined in silico by assembling EST BF699808 and 5'-truncated FLJ39221 cDNA. Nucleotide sequence of mouse Lasp2 cDNA was derived from 1200007O21Rik cDNA. Human LASP2 (270 aa) showed 97.4% and 63.7% total-amino-acid identity with mouse Lasp2 and human LASP1, respectively. LASP2 and LASP1 were the LASP family proteins consisting of LIM domain, Nebulin repeat, and SH3 domain. LASP2 and NEBL mRNAs were transcribed from the LASP2/NEBL gene on human chromosome 10p12 due to alternative splicing. LASP2 mRNA consists of exons 1a-4a, 24, 27, and 28 of the LASP2/NEBL gene, while NEBL mRNA consists of exons 1-28. Exon 1a-4a of the LASP2/NEBL gene were more homologous to exon 1-4 of the LASP1 gene on human chromosome 17q12, while exon 1-28 of the LASP2/NEBL gene were more homologous to exons of NEB gene on human chromosome 2q23. Some part of the LASP2/ NEBL-TEM7L-ARL8-CACNB2 locus on 10p12 was paralogous to the LASP1-TEM7-CACNB1 locus on 17q12, while the other part of the LASP2/NEBL-TEM7L-ARL8-CACNB2 locus was paralogous to the NEB-ARL5-CACNB4 locus on 2q23. These facts indicate that the LASP2/NEBL-TEM7L-ARL8-CACNB2 is a chimeric locus, which might be generated through the homologous recombination between the ancestral lasp2-tem7l-cacnb2 locus and the ancestral nebl-arl8 locus. Therefore, gene fusion during evolution is one of the mechanisms to generate alternative splicing.

Adaptor Proteins, Signal Transducing↗