Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements

The olfactory receptor (OR)-gene superfamily is the largest in the mammalian genome. Several of the human OR genes appear in clusters with > or = 10 members located on almost all human chromosomes, and some chromosomes contain more than one cluster. We demonstrate, by experimental and in silico data, that unequal crossovers between two OR gene clusters in 8p are responsible for the formation of three recurrent chromosome macrorearrangements and a submicroscopic inversion polymorphism. The first two macrorearrangements are the inverted duplication of 8p, inv dup(8p), which is associated with a distinct phenotype, and a supernumerary marker chromosome, +der(8)(8p23.1pter), which is also a recurrent rearrangement and is associated with minor anomalies. We demonstrate that it is the reciprocal of the inv dup(8p). The third macrorearrangment is a recurrent 8p23 interstitial deletion associated with heart defect. Since inv dup(8p)s originate consistently in maternal meiosis, we investigated the maternal chromosomes 8 in eight mothers of subjects with inv dup(8p) and in the mother of one subject with +der(8), by means of probes included between the two 8p-OR gene clusters. All the mothers were heterozygous for an 8p submicroscopic inversion that was delimited by the 8p-OR gene clusters and was present, in heterozygous state, in 26% of a population of European descent. Thus, inversion heterozygosity may cause susceptibility to unequal recombination, leading to the formation of the inv dup(8p) or to its reciprocal product, the +der(8p). After the Yp inversion polymorphism, which is the preferential background for the PRKX/PRKY translocation in XX males and XY females, the OR-8p inversion is the second genomic polymorphism that confers susceptibility to the formation of common chromosome rearrangements. Accordingly, it may be possible to develop a profile of the individual risk of having progeny with chromosome rearrangements.     

Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements

Canine tricuspid valve malformation (CTVM) maps to canine chromosome 9 (CFA9), in a region syntenic with gene-dense human chromosome 17q. To define synteny blocks, we analyzed 148 markers on CFA9 using radiation hybrid mapping and established a four-way comparative map for human, mouse, rat, and dog. We identified a large number of rearrangements, allowing us to reconstruct the evolutionary history of individual synteny blocks and large chromosomal segments. A most parsimonious rearrangement scenario for all four species reveals that human chromosome 17q differs from CFA9 and the syntenic rodent chromosomes through two macroreversals of 9.2 and 23 Mb. Compared to a recovered ancestral gene order, CFA9 has undergone 11 reversals of <3 Mb and 2 reversals of >3 Mb. Interspecies reuse of breakpoints for micro- and macrorearrangements was observed. Gene order and content of the ctvm interval are best extrapolated from murine data, showing that multispecies genome rearrangement scenarios contribute to identifying gene content in canine mapping studies.     

Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates

We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1.23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size.     

Unstable chromosome sites and evolutionary rearrangements in akodont rodents (Cricetidae)

Evolutionary rearrangements producing changes in chromosome 1 of Akodon molinae were traced by comparing the G banding patterns of the karyotypes from six species of akodont rodents. It was possible to subdivide chromosome 1 of A. molinae into unstable and stable regions. Most of the spontaneous rearrangements of chromosome 1 appearing in passages 116-128 of a continuous line of A. molinae cells (AKm line) occurred in the unstable regions which comprise repetitive DNA sequences favouring the setting up of heteroduplexes leading to rearrangements. When AKm cells were irradiated with UV light it was observed that unstable regions of chromosome 1 showed higher rates of unscheduled DNA synthesis (UD) than stable areas. A differential degree of condensation making certain regions of the chromatin fibril more accessible to repair enzymes or a better target for damage, is probably the cause of the variable response to UV light, and perhaps to most clastogenic agents (including those responsible for spontaneous rearrangements). Thus, the distribution of repetitive DNA sequences, the structure of the chromatin fibril and the efficiency of the DNA repair machinery may be important factors in the origin of spontaneous chromosomal rearrangements.     

Ancient genomic architecture for mammalian olfactory receptor clusters

Background  

Mammalian olfactory receptor (OR) genes reside in numerous genomic clusters of up to several dozen genes. Whole-genome sequence alignment nets of five mammals allow their comprehensive comparison, aimed at reconstructing the ancestral olfactory subgenome.     

The evolutionary history of human chromosome 7

We report on a comparative molecular cytogenetic and in silico study on evolutionary changes in human chromosome 7 homologs in all major primate lineages. The ancestral mammalian homologs comprise two chromosomes (7a and 7b/16p) and are conserved in carnivores. The subchromosomal organization of the ancestral primate segment 7a shared by a lemur and higher Old World monkeys is the result of a paracentric inversion. The ancestral higher primate chromosome form was then derived by a fission of 7b/16p, followed by a centric fusion of 7a/7b as observed in the orangutan. In hominoids two further inversions with four distinct breakpoints were described in detail: the pericentric inversion in the human/African ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzee. FISH analysis employing BAC probes confined the 7p22.1 breakpoint of the pericentric inversion to 6.8 Mb on the human reference sequence map and the 7q22.1 breakpoint to 97.1 Mb. For the paracentric inversion the breakpoints were found in 7q11.23 between 76.1 and 76.3 Mb and in 7q22.1 at 101.9 Mb. All four breakpoints were flanked by large segmental duplications. Hybridization patterns of breakpoint-flanking BACs and the distribution of duplicons suggest their presence before the origin of both inversions. We propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements.     

嗅觉受体基因的研究进展

嗅觉在动物的生命活动中起着重要的作用, 与嗅觉相关的基因主要是嗅觉受体(Olfactory receptor, OR)基因。文章介绍了嗅觉受体基因的结构、表达调控、分布、分子进化及其多态性研究进展, 并讨论了该基因与嗅觉功能和嗅觉障碍的关系。     

红色红曲菌M7核型分析与桔霉素、色素基因簇的染色体定位

以红色红曲菌Monascus ruber M7菌株为研究对象,对其核型进行分析,并将桔霉素与色素合成基因簇定位于染色体。通过原生质体制备,以脉冲场凝胶电泳进行核型分析。在此基础上,通过Southern杂交将桔霉素与色素合成基因簇定位于染色体。脉冲场凝胶电泳结果显示,红色红曲菌M7包含大小依次为4.9,4.3,3.7,3.4,3.0,2.3,2.1Mb的7条(I-VII)染色体,基因组大小约为23.7Mb。Southern杂交结果表明,桔霉素合成基因簇位于第IV条染色体上,色素合成基因簇位于第V条染色体上。     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

The complement factor 5a receptor gene maps to murine chromosome 7

Complement factor 5a (C5a) promotes local inflammation and is a potent chemoattractant for neutrophils and macrophages. We had an interest in C5a and its receptor, C5r1, because we previously identified C5a as a positional candidate gene for the quantitative trait locus Abhr2, which determines allergen-induced bronchial hyperresponsiveness in our murine model of asthma. To study the significance of C5r1 in our asthma model we first had to determine its genomic map location in mice. Genomic sequence surrounding murine C5r1 was analyzed for polymorphisms and two variable microsatellites were identified. These microsatellites were genotyped in A/J x (C3H/HeJ x A/J)F1 backcross mice (n = 355) and mapped in a panel of 164 markers spaced at approximately 10 cM intervals throughout the genome. Multipoint linkage analysis placed C5r1 on murine chromosome 7, 3.9 cM from the top of the linkage group. This map location has been previously identified as containing an additional quantitative trait locus for allergen-induced airway hyperresponsiveness, Abhr3, in this population of mice.     

Integrated olfactory receptor and microarray gene expression databases

Background  

Gene expression patterns of olfactory receptors (ORs) are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD) to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB), which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction.     

A mapping and evolutionary study of porcine sex chromosome gene

A combination of FISH and RH mapping was used to study the evolution of sex chromosome genes in the pig. In total, 19 genes were identified, including 3 PAR genes (STS, KAL, PRK). The gene order of the porcine X Chromosome (Chr) closely resembled the human X Chr (PRK/STS/KAL–AMELX–EIF2s3X/ZFX–USP9X–DBX–SMCX), suggesting that the porcine X has undergone very little rearrangement during evolution. For the porcine Y Chr, two linkage groups of 10 NRY genes were found, and the following order was established: Ypter–(AMELY–EIF2S3Y/ZFY–USP9Y–DBY/UTY)–(TSPY–SMCY–UBE1Y–SRY)–CEN. This gene order showed greater conservation with the murine Y than with the human Y Chr. In addition, all porcine Y Chr genes mapped to Yp, which is similar to the mouse and included EIF2s3Y and UBE1Y, which are not present in humans. Interestingly, complete conservation of X/Y homologous gene order was found between the pig X and Y Chrs, indicating that the porcine Y Chr has not undergone extensive reorganisation with respect to the X. This suggests that the order of the X/Y homologous genes of the porcine X and Y Chrs may closely resemble the ancestral gene order of the eutherian sex chromosomes.     

A human T-cell antigen receptor beta chain gene maps to chromosome 7.

cDNA clones which encode the human and mouse T cell antigen receptor beta chain gene have previously been isolated. We have used a mouse cDNA clone to map the chromosomal position of a human beta chain gene. Southern blot analysis of DNA prepared from somatic cell hybrids has assigned this gene to chromosome 7. The use of a hybrid containing a chromosome 7 translocation has further localised this gene to the region 7q22-qter.     

The gene orders on human chromosome 15 and chicken chromosome 10 reveal multiple inter- and intrachromosomal rearrangements

Comparative mapping between the human and chicken genomes has revealed a striking conservation of synteny between the genomes of these two species, but the results have been based on low-resolution comparative maps. To address this conserved synteny in much more detail, a high-resolution human-chicken comparative map was constructed from human chromosome 15. Mapping, sequencing, and ordering of specific chicken bacterial artificial chromosomes has improved the comparative map of chromosome 15 (Hsa15) and the homologous regions in chicken with almost 100 new genes and/or expressed sequence tags. A comparison of Hsa15 with chicken identified seven conserved chromosomal segments between the two species. In chicken, these were on chromosome 1 (Gga1; two segments), Gga5 (two segments), and Gga10 (three segments). Although four conserved segments were also observed between Hsa15 and mouse, only one of the underlying rearrangement breakpoints was located at the same position as in chicken, indicating that the rearrangements generating the other three breakpoints occurred after the divergence of the rodent and the primate lineages. A high-resolution comparison of Gga10 with Hsa15 identified 19 conserved blocks, indicating the presence of at least 16 intrachromosomal rearrangement breakpoints in the bird lineage after the separation of birds and mammals. These results improve our knowledge of the evolution and dynamics of the vertebrate genomes and will aid in the clarification of the mechanisms that underlie the differentiation between the vertebrate species.     

Immunoglobulin and T cell receptor gene rearrangements in lymphoproliferative disorders

Thirty-one samples representing Hodgkin's and non-Hodgkin's lymphomas, angioimmunoblastic lymphadenopathy (AILD), and benign follicular hyperplasia in HIV infections were examined for rearrangements of the immunoglobulin (Ig) and T cell receptor (TcR) beta-chain gene loci. In 11 of 12 non-Hodgkin's lymphomas (classified as Burkitt lymphoma (2), centrocytic lymphoma (1), centrocytic-centroblastic lymphoma (5), centroblastic lymphoma (3], only rearranged Ig genes could be detected. The exceptional case was an unclassified high-grade lymphoma, which represented a rearrangement of the TcR beta-chain. We also examined DNA from lymphoid neoplasms in which the lineage of the malignant cell was still controversial. Rearrangement of the TcR could exclusively be demonstrated in all 3 cases of AILD. One Ig gene rearrangement and 4 TcR beta-chain rearrangements were found in 13 samples of Hodgkin's lymphomas (11 lymph nodes, 1 pleura effusion and 1 bone biopsy with proven infiltration). Examination of 3 cases of benign follicular hyperplasia in HIV infection represented one Ig rearrangement.     

Organization and evolutionary relatedness of OR37 olfactory receptor genes in mouse and human

We report a comprehensive comparative analysis of human and mouse olfactory receptor (OR) genes encoding OR37 subtypes to determine the repertoire, chromosomal organization, and relatedness of these genes. Two OR37 clusters were found in both mouse (chromosome 4) and human (chromosome 9); with five genes in cluster I and three (mouse) and seven genes (human) in cluster II. The pronounced diversity of noncoding sequence regions in both genomic loci indicates a long-term coexistence of the two clusters and the genes within the clusters. In contrast, the coding regions, particularly of genes in cluster I, showed remarkably high sequence identity, a feature quite unique for OR genes. The conservation of only the coding sequences indicates that OR37 may be under negative selection pressure and suggests that the OR37 receptor family may be tuned to recognize distinct sets of signaling molecules. A comparison of mouse and human OR37 gene clusters revealed that genes in cluster I are highly related within each species whereas genes in cluster II are highly related across species. These data reflect a unique and complex evolutionary history of the OR37 family.