DNA sequence : the journal of DNA sequencing and mapping最新文献

Zinc finger protein, one of the most important transcription factors, plays an essential role in regulating gene expression. C(2)H(2) type zinc protein with KRAB domain contains two parts, one is C(2)H(2) zinc finger motif which is use to binding to the DNA, while the other is KRAB associated box which mostly performs as a transcription repressor. In this study, we report the cloning and characterization of a novel splice variant of the human ZNF300 gene (ZNF300-B). The ZNF300-B gene cDNA is 2293 bp in length, encoding a putative protein with 619 amino acid residues. ZNF300-B gene is mapped to chromosome 5q32-5q33 with seven exons. Reverse transcription polymerase chain reaction (RT-PCR) analysis showed that ZNF300-B and ZNF-300 were expressed highly in human testis.

The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. The mitochondrial DNA was 16,659 base pairs (bp) in length. Sequence features of the 13 protein-coding genes, two ribosomal RNAs and 22 transfer RNAs are described. The non-coding control region (1017 bp) was compared with those of the closely related soles Solea solea and Solea lascaris. The typical conservative blocks were identified. A cluster of 42 and 22 tandemly arrayed repeats was detected near the 3' end of control region in S. solea and S. lascaris, respectively. On the contrary, only two (93.8% of haplotypes) or three copies (6.2%) of an 8-bp repeated sequence motif was found in S. senegalensis. Phylogenetic analysis showed that 7 out of 9 of haplotypes bearing three copies grouped in a separate cluster. Possible mechanisms influencing the evolution of control region among soles are discussed.

We characterized a novel gene, AmphiCaBP-like, encoding a putative Ca(2 + )-binding protein (CaBP) with three EF-hand motifs from amphioxus (Branchiostoma belcheri tsingtauense). It exhibits significant similarities with the calmodulin and troponin C proteins from other species. Results of phylogenetic analysis indicated that amphioxus AmphiCaBP-like falls on the base of the troponin C clade. It may be a novel member of the calmodulin-like subfamily. In situ hybridization and RT-PCR analysis showed that AmphiCaBP-like is expressed throughout early development except the stages around the blastula. From neurula stage onward, transcripts of the AmphiCaBP-like are detected in the neural plate, the neural tube, the differentiating somites and the splanchnopleure, as well as the epithelium of the pharynx and gut. It is also expressed in the presumptive, but not the well-developed notochord. In adult amphioxus, the transcripts are found in the epithelial cells of the gut and midgut diverticulus, the wall of coelom, the branchia, the neural cord and gonads.

The growth-correlated genes that are part of the neuroendocrine growth axis play crucial roles in the regulation of growth and development of pig. The identification of genetic polymorphisms in these genes will enable the scientist to evaluate the biological relevance of such polymorphisms and to gain a better understanding of quantitative traits like growth. In the present study, seven pairs of primers were designed to obtain unknown sequences of growth-correlated genes, and other 25 pairs of primers were designed to identify single nucleotide polymorphisms (SNP) using the denaturing high-performance liquid chromatography (DHPLC) technology in four pig breeds (Duroc, Landrace, Lantang and Wuzhishan), significantly differing in growth and development characteristics. A total of 101 polymorphisms were discovered in 10,707 base pairs (bp) from six genes of the ghrelin (GHRL), leptin (LEP), insulin-like growth factor II (IGF-II), insulin-like growth factor binding protein 2 (IGFBP-2), insulin-like growth factor binding protein 3 (IGFBP-3), and somatostatin (SS). The observed average distances between the SNP in the 5'UTR, coding regions, introns and 3'UTR were 134, 521, 81 and 92 bp, respectively. Four SNPs were found in the coding regions of IGF-II, IGFBP-2 and LEP, respectively. Two synonymous mutations were obtained in IGF-II and LEP genes respectively, and two non-synonymous were found in IGFBP-2 and LEP genes, respectively. Seven other mutations were also observed. Thirty-two PCR-RFLP markers were found among 101 polymorphisms of the six genes. The SNP discovered in this study would provide suitable markers for association studies of candidate genes with growth related traits in pig.

Asthma is a common respiratory disease that is driven by both genetic and environmental factors. Identification of the genes underlying asthma will provide insight into the mechanisms and treatment of this important disease. Previous studies in this laboratory identified two distinct quantitative trait loci for the asthma-related parameter, allergen-induced airway hyperresponsiveness, in a murine model by means of a genome-wide linkage analysis. The present study focuses and refines the map location of these two loci. Additionally, we explore prostaglandin-endoperoxide synthase-1 (Ptgs1) and mannose receptor C-type 1 (Mrc1) genes as two new positional candidate genes for allergen-induced airway hyperresponsiveness through comparative sequence analysis and mRNA expression studies of mouse strains with genetically mediated airway responsiveness.

We are investigating the genetic basis of morphological differences in skull shape between domestic dogs of different breeds using a candidate gene approach to identify genes involved in the genetic regulation. One such candidate is Fgf8. Fgf8 is a signalling molecule important in the embryonic development and patterning of the craniofacial region. Mice conditional null for the expression of Fgf8 after E9.5 have a short foreface and a wide skull (Trumpp et al. 1999). Using a combination of bioinformatics and PCR cloning, we have characterised the genomic loci of the canine Fgf8 gene. Like the mouse homologue, it is composed of six exons and we also predict that like the mouse, there are eight alternative isoforms that are generated by alternative splicing events. We have identified a short 200 bp sequence upstream of the Fgf8 gene that is highly conserved between species and have predicted putative transcription factor binding sites using the Transfac database. Genetic analysis of 4 dogs with different skull types identified genetic variation. None of the variants however, were predicted to have any functional significance.

Two new cDNAs, human GPR107 and murine GPR108, were cloned from mammalian lung that are members of a novel gene family encoding proteins that are predicted to have an amino-terminal hydrophobic signal peptide sequence, a long extracellular domain and a carboxy-terminal seven transmembrane domain (LUSTR domain) similar to GPCRs. The 18-exon human GPR107 gene is located at 9q34.2-3 and spans 86.4 kb and the cDNA encodes a 552 residue protein. The closely related, but not homologous, 17-exon murine Gpr108 gene is located at 17C-D and spans 12.8 kb. The murine Gpr108 cDNA encodes a 562 residue protein that has 49% identity to human GPR107. They are distantly related to two other genes, transmembrane protein 87A and 87B that encode LUSTR domain-containing proteins in the human genome. LUSTR proteins are also found in Drosophila, Saccharomyces and Arabidopsis, but are absent from bacteria, archaea and viruses. This suggests that GPCRs are present in higher plants.

A novel splice variant of human AP3B2, named AP3B2_v2, was isolated through the large-scale sequencing analysis of a human fetal brain cDNA library. The AP3B2_v2 cDNA is 1171 bp in length. Sequence analysis revealed AP3B2_v2 missed 22 exons that existed in AP3B2_v1, leading to a different putative protein. The deduced proteins were 145 amino acids (designated as AP3B2_v2) and 1082 amino acids (AP3B2_v1) in length, sharing the C-terminal 145 amino acids. RT-PCR analysis showed that human AP3B2_v2 were expressed in several human adult tissues analyzed. The expression levels of AP3B2_v2 were relatively high in brain and testis. In contrast, low levels of expression were detected in kidney, pancreas, spleen, thymus, prostate, ovary and small intestine.

The complete coding sequence of Hemonchus contortus HC58cDNA was generated by rapid amplification of cDNA ends and polymerase chain reaction using primers based on the 5' and 3' ends of the parasite mRNA, accession no. AF305964. The HC58cDNA gene was 851 bp long, with open reading frame of 717 bp, precursors to 239 amino acids coding for approximately 27 kDa protein. Analysis of amino acid sequence revealed conserved residues of cysteine, histidine, asparagine, occluding loop pattern, hemoglobinase motif and glutamine of the oxyanion hole characteristic of cathepsin B like proteases (CBL). Comparison of the predicted amino acid sequences showed the protein shared 33.5-58.7% identity to cathepsin B homologues in the papain clan CA family (family C1). Phylogenetic analysis revealed close evolutionary proximity of the protein sequence to counterpart sequences in the CBL, suggesting that HC58cDNA was a member of the papain family.

A cDNA library was constructed in lambda TriplEx2 vector using poly (A(+)) RNA from immature seeds of Cicer arietinum. The lectin gene was isolated from seeds of chickpea through library screening and RACE-PCR. The full-length cDNA of Chichpea seed lectin(CpGL)is 972 bp and contains a 807 bp open reading frame encoding a 268 amino acid protein. Analysis shows that CpSL gene has strong homology with other legume lectin genes. Phylogenetic analysis showed the existence of two main clusters and clearly indicated that CpSL belonged to mannose-specific family of lectins. RT-PCR revealed that CAA gene expressed constitutively in various plant tissues including flower, leaf, root and stem. When chickpea lectin mRNA level was checked in developing seeds, it was higher in 10 DAF seeds and decreased throughout seed development.