Rattus norvegicus melanocortin 3 receptor: a corrected sequence

Examination of the Rattus norvegicus genome reveals differences in the melanocortin 3 receptor (MC3R) compared with the published sequence (accession X70667). To clarify these differences, we used RT-PCR to clone MC3R from Sprague Dawley rats. These efforts revealed a sequence for the rat MC3R consistent with that predicted by the rat genome, but different from the published receptor by three amino acids, all of which were located in the predicted second transmembrane domain (TM2). Analysis of these residues revealed that TM2 of the rat MC3R is more homologous with other species than previously considered. The presently described sequence maps onto chromosome 3 of the rat genome, which shows highly conserved synteny with the mouse chromosome 2 and the human chromosome 20. Transient expression revealed high affinity binding of [125I]-NDP-MSH and a concentration-dependent cAMP response to the synthetic agonist MTII. These data both clarify the sequence of the MC3R and demonstrate the great utility of genomic information recently made available.     

Linkage map of two HLA-SB beta and two HLA-SB alpha-related genes: an intron in one of the SB beta genes contains a processed pseudogene

Three overlapping cosmid clones contain coding sequences for four HLA Class II genes, provisionally identified as two HLA-SB alpha and two HLA-SB beta genes. The genes are in the order beta, alpha, beta, alpha, inverted with respect to each other. One of the SB beta genes contains a 513 bp sequence that appears to be a processed pseudogene, flanked by direct 17 bp repeat sequences, in the intron upstream of the beta 1 exon. The pseudogene is homologous to a family of sequences of approximately 25-40 members, most of which are not on chromosome 6. A cDNA clone, highly homologous to the pseudogene, except for its 5' end, contains a normal poly(A) addition site and a poly(A) tail. The cDNA clone is homologous to a single-copy gene in both man and mouse, encoded on human chromosome 15. A search of published DNA sequences identified a mouse sequence, with about 77% similarity to the pseudogene sequence, in the negative strand of an intron in a mouse dihydrofolate reductase gene. The second SB beta gene does not contain the pseudogene sequence.     

Confirmation, via in situ hybridization, of the occurrence of Robertsonian translocations during lemur evolution by localization of GLUDP1 DNA sequences on lemur chromosomes.

A human genomic DNA sequence derived from glutamate dehydrogenase pseudogene 1 was used as a probe for in situ hybridization to the chromosomes of three lemur species, Eulemur fulvus mayottensis (EFU), E. macaco macaco (EMA), and E. coronatus (ECO). This sequence, which is 98% homologous to the nucleotide sequence of the gene for human glutamate dehydrogenase (GLUD), was found on homologous bands of three morphologically similar chromosome segments, EFU14, EMA5p, and ECO8q, confirming that different Robertsonian translocations occurred during the evolution of these three species. These loci on the lemur chromosomes probably correspond to the human GLUD locus.     

A DNA sequence that is present in both sexes of Artiodactyla is repeated on the Y chromosome of cattle, sheep, and goats

We have cloned a 307-bp Sau3AI fragment of DNA from the bovine male genome by deletion enrichment. Although a single-copy homolog is present in the female cattle genome, the sequence (BRY.1) is repeated at a moderate and variable frequency only in males. This pattern occurs too in sheep and goats, but BRY.1 is found in equal amounts in both sexes of fallow deer and pigs, approximating single copy. The conservation of a homologous sequence over millions of years and its repetition exclusively on the Bovidae Y chromosome raise interesting questions concerning the origin, evolution, and possible function of this unusual element.     

The species and chromosomal distribution of the centromeric alpha-satellite I sequence from sheep in the tribe Caprini and other Bovidae

The evolution of chromosomes in species in the family Bovidae includes fusion and fission of chromosome arms (giving different numbers of acrocentric and metacentric chromosomes with a relatively conserved total number of arms) and evolution in both DNA sequence and copy number of the pericentromeric alpha-satellite I repetitive DNA sequence. Here, a probe representing the sheep alpha-satellite I sequence was isolated and hybridized to genomic DNA digests and metaphase chromosomes from various Bovidae species. The probe was highly homologous to the centromeric sequence in all species in the tribe Caprini, including sheep (Ovis aries), goat (Capra hircus) and the aoudad or Barbary sheep (Amnotragus lervia), but showed no detectable hybridization to the alpha-satellite I sequence present in the tribe Bovini and at most very weak to species in the tribes Hippotragini, Alcelaphini or Aepycerotini. The sex chromosomes of sheep, goat and aoudad did not contain detectable alpha-satellite I sequence; in sheep, one of the three metacentric autosomal chromosomes does not carry the sequence, while in aoudad, it is essentially absent in three large autosomal pairs as well as the large metacentric chromosome pair. The satellite probes can be used as robust chromosome and karyotype markers of evolution among tribes and increase the resolution of the evolutionary tree at the base of the Artiodactyla.     

Sequence of specific mitochondrial 16S rRNA gene fragment from Egyptian buffalo is used as a pattern for discrimination between river buffaloes,cattle, sheep and goats

Characterization of molecular markers and the development of better assays for precise and rapid detection of domestic species are always in demand. This is particularly due to recent food scares and the crisis of biodiversity resulting from the huge ongoing illegal traffic of endangered species. The aim of this study was to develop a new and easy method for domestic species identification (river buffalo, cattle, sheep and goat) based on the analysis of a specific mitochondrial nucleotide sequence. For this reason, a specific fragment of Egyptian buffalo mitochondrial 16S rRNA gene (422 bp) was amplified by PCR using two universal primers. The sequence of this specific fragment is completely conserved between all tested Egyptian buffaloes and other river buffaloes in different places in the world. Also, the lengths of the homologous fragments were less by one nucleotide (421 bp) in case of goats and two nucleotides (420 bp) in case of both cattle and sheep. The detection of specific variable sites between investigated species within this fragment was sufficient to identify the biological origin of the samples. This was achieved by alignment between the unknown homologous sequence and the reference sequences deposited in GenBank database (accession numbers, FJ748599–FJ748607). Considering multiple alignment results between 16S rRNA homologous sequences obtained from GenBank database with the reference sequence, it was shown that definite nucleotides are specific for each of the four studied species of the family Bovidae. In addition, other nucleotides are detected which can allow discrimination between two groups of animals belonging to two subfamilies of family Bovidae, Group one (closely related species like cattle and buffalo, Subfamily Bovinae) and Group two (closely related species like sheep and goat, Subfamily Caprinae). This 16S DNA barcode character-based approach could be used to complement cytochrome c oxidase I (COI) in DNA barcoding. Also, it is a good tool for identification of unknown sample belonging to one of the four domestic animal species of family Bovidae quickly and easily.     

用放射杂交板定位鸡的MC4R基因以及其在鸡和人染色体上同源区的比较分析

黑素皮质素受体(melanocortin-4 receptor,MC4R)基因的突变与猪、鼠和人等的食欲、肥胖和生长有关联性,然而对鸡的MC4R基因的功能却知之甚少。为了确定鸡的MC4R基因在染色体上的位置,使用鸡-仓鼠杂交板(ChickRH6)做了该基因的定位工作。通过扩增ChickRH6杂交板上的93个样品,然后经整合分析将mC4R基因定位在2号染色体上的标记MCW0062、BCL2和OVY附近,即2q12。这个连锁图上的5个标记基于两点分析与MC4R的LOD值都大于5。同时,以MC4R基因为标记做了鸡和人的染色体比较分析。结果显示鸡的2号染色体(GGA2)和人的18号染色体(HSA18)存在同源区,且基因BCL2和肥胖基因(obesity)位于MC4R基因附近。推测鸡的MC4R基因与人的MC4R基因可能具有相似的功能。该研究揭示了鸡和人MC4R基因的染色体分布,并用杂交放射板将鸡的MC4R基因定位在2号染色体的12区带。     

Contribution of melanocortin receptor exoloops to Agouti-related protein binding.

Agouti-related protein (AGRP) is an endogenous antagonist of melanocortin action that functions in the hypothalamic control of feeding behavior. Although previous studies have shown that AGRP binds three of the five known subtypes of melanocortin receptor, the receptor domains participating in binding and the molecular interactions involved are presently unknown. The present studies were designed to examine the contribution of extracytoplasmic domains of the melanocortin-4 receptor (MC4R) to AGRP binding by making chimerical receptor constructs of the human melanocortin-1 receptor (MC1R; a receptor that is not inhibited by AGRP) and the human MC4R (a receptor that is potently inhibited by AGRP). Substitutions of the extracytoplasmic NH2 terminus and the first extracytoplasmic loop (exoloop) of the MC4R with homologous domains of the MC1R had no effect on AGRP (87-132) binding affinity or inhibitory activity (the ability to inhibit melanocortin-stimulated cAMP generation). In contrast, cassette substitutions of exoloops 2 and 3 of the MC4R with the homologous exoloops of the MC1R resulted in a substantial loss of AGRP binding affinity and inhibitory activity. Conversely, the exchange of exoloops 2 and 3 of the MC1R with the homologous exoloops of the MC4R was found to confer AGRP binding and inhibitory activity to the basic structure of the MC1R. Importantly, these substitutions did not affect the ability of the alpha-melanocyte stimulating hormone analogue [Nle4,D-Phe7] melanocyte stimulating hormone to bind or activate the chimeric receptors. These data indicate that exoloops 2 and 3 of the melanocortin receptors are important for AGRP binding.     

Members of the human glyceraldehyde-3-phosphate dehydrogenase-related gene family map to dispersed chromosomal locations

Several highly homologous glyceraldehyde-3-phosphate dehydrogenase (GAPD)-related sequences have been identified previously in human DNA by Southern blot analysis. Protein studies have identified only a single expressed locus for this major glycolytic enzyme, and this maps to chromosome 12p13. Sequence analysis of a GAPD muscle cDNA clone and a GAPD-related clone retrieved from an X-chromosome recombinant library showed that the latter was a processed pseudogene that maps to Xp11-p21. In this study, we have determined the chromosomal locations of several of the additional GAPD-related human sequences using a short 3' end sequence from the cDNA to probe DNA from a series of human-rodent somatic cell hybrids on Southern blots. Eight HindIII GAPD-related sequences detected at high stringency have been mapped to 6 different chromosomes. Several of the additional sequences detected at more moderate stringency have been localized to a further 10 chromosomal sites. Together, these sites constitute the known expressed locus, the known X-linked pseudogene, and 15 GAPD-like loci.     

The melanocyte-stimulating hormone receptor (MC1-R) gene as a tool in evolutionary studies of artiodactyles

The complete coding region of the melanocyte-stimulating hormone receptor (MC1-R) gene was characterized in species belonging to the two families Bovidae and Cervidae; cattle (Bos taurus), sheep (Ovis aries), goat (Capra hircus), muskox (Ovibos moschatus), roe deer (Capreolus capreolus), reindeer (Rangifer tarandus), moose (Alces alces), red deer (Cervus elaphus) and fallow deer (Dama dama). This well conserved gene is a central regulator of mammalian coat colour. Examination of the interspecies variability revealed a 5.3-6.8% divergence between the Cervidae and Bovidae families, whereas the divergence within the families were 1.0-3.1% and 1.2-4.6%, respectively. Complete identity was found when two subspecies of reindeer, Eurasian tundra reindeer (R.t. tarandus) and Svalbard reindeer (R.t. platvrhynehus), were analyzed. An rooted phylogenetic tree based on Bovidae and Cervidae MC1-R DNA sequences was in complete agreement with current taxonomy, and was supported by bootstrapping analysis. Due to different frequencies of silent vs. replacement mutations, the amino acid based phylogenetic tree contains several dissimilarities when compared to the DNA based phylogenetic tree.     

Pstl repeat: a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo.

The PstI family of elements are short, highly repetitive DNA sequences interspersed throughout the genome of the Bovidae. We have cloned and sequenced some members of the PstI family from cattle, goat, and buffalo. These elements are approximately 500 bp, have a copy number of 2 x 10(5) - 4 x 10(5), and comprise about 4% of the haploid genome. Studies of nucleotide sequence homology indicate that the buffalo and goat PstI repeats (type II) are similar types of short interspersed nucleotide element (SINE) sequences, but the cattle PstI repeat (type I) is considerably more divergent. Additionally, the goat PstI sequence showed significant sequence homology with bovine serine tRNA, and is therefore likely derived from serine tRNA. Interestingly, Southern hybridization suggests that both types of SINEs (I and II) are present in all the species of Bovidae. Dendrogram analysis indicates that cattle PstI SINE is similar to bovine Alu-like SINEs. Goat and buffalo SINEs formed a separate cluster, suggesting that these two types of SINEs evolved separately in the genome of the Bovidae.     

Presence of a human Hyaluronan binding protein 1 (HABP1) pseudogene-like sequence in Methanosarcina barkeri suggests its linkage in evolution

The gene encoding Hyaluronan binding protein 1 (HABP1) and its homologs have been reported across eukaryotes, from yeast to human. We have reported the presence of processed pseudogenes in several human chromosomes, along with the location of the HABP1 gene on chromosome 17p12-p13. In this study, we report not only the presence of HABP1 pseudogene in other animal species, but also the presence of a homologous sequence in Methanosarcina barkeri, an ancient life form. This sequence has 44.8% homology to the human HABP1 cDNA and 45.3% homology with the HABP1 pseudogene in human chromosome 21. This sequence has a high G + C content (57%), characteristic of archaea, a family to which M. barkeri belongs. The presence of this HABP1 cDNA like fragment in M. barkeri might enable us to shed light on the evolution of the HABPl gene and whether it was present in a common ancestral organism before the lineages separated.     

Identification in human genomic DNA of the sequence homologous but not identical to either the histo-blood group ABH genes or alpha 1----3 galactosyltransferase pseudogene

Based on polymerase chain reaction (PCR) and sequencing of the cloned amplified fragments, we identified a homologous sequence to the histo-blood group ABH genes and alpha 1----3 galactosyltransferase pseudogene. The presence of this sequence in human genomic DNA was confirmed by Southern hybridization.     

A unique structure of a mouse gamma-actin processed pseudogene

We have isolated several gamma-actin-related genes from a mouse genomic library. One of these has been shown to be a gamma-actin processed pseudogene (Tokunga, K., Yoda, K. and Sakiyama, S. (1985) Nucleic Acids Res. 13, 3031-3042). Here, we report the structure of another pseudogene (pMA131). pMA131 contained the sequences corresponding to the carboxyl half of a cytoskeletal actin in which random point mutations as well as insertion and deletion events took place. This region was flanked at its 5' end by the sequences related to mouse repetitive sequences, including the MIF-1 family, and was interrupted by the sequence homologous to the R family which is also a mouse repetitive sequence. The coding region was followed by the sequence corresponding to 3' untranslated region of gamma-actin mRNA.     

Nucleotide sequence of a portion of human chromosome 9 containing a leukocyte interferon gene cluster

The nucleotide sequence of a 9937 base-pair portion of human chromosome 9, which contains two complete leukocyte interferon genes (LeIF-L and J), the complete intergenic region, and part of a third related possible pseudogene (LeIF-M), has been determined. The coding regions of the L and J genes are separated by 4363 nucleotides. The coding regions for the putative L and J interferons are 96% homologous and are each surrounded by about 3500 nucleotides of flanking sequences, which are also highly homologous. The L and J genes and their respective flanking sequences comprise a 4000 nucleotide leukocyte interferon gene repeat unit; the L gene repeat unit contains two major insertions not present in the J gene repeat unit. The J gene repeat unit is flanked by sequence features reminiscent of those found surrounding transposable elements. Both the L and J gene repeat units are embedded within sequences that are highly repeated in the human genome. Structural features identified within this portion of chromosome 9 may have been important for the generation of this interferon gene cluster.