Pub Date : 2002-01-01DOI: 10.1080/10425170290019838
Yuxin Fan, Long Yu, Q. Tu, Ruomu Gong, Ying Jiang, Qi Zhang, F. Dai, Chiyuan Chen, Shouyuan Zhao
In the present study, a brain abundant member of g 4-galactosyltransferase gene family with an open reading frame encoding 343 amino acids was cloned and identified from a human leukemia cell cDNA library. The putative protein sequence is about 94.8 and 94.2% identical to the 382-amino-acid mouse and rat g 4-galactosyltransferase respectively and also contains cysteine residues previously shown to be important for the function of the gene family members. This cDNA (tentatively termed g 4GalT-VIb) is identical to a recently reported cDNA (tentatively termed g 4GalT-VIa) of human g 4-galactosyltransferase except lacking one exon, suggesting that these two cDNAs are two different alternative transcripts of the same gene. Northern hybridization showed that the new alternative transcript, g 4GalT-VIb, is expressed in all 16 human tissues tested with highest level in brain and rich level in testis, thymus and pancreas, whereas weak expression was detected in lung. The g 4GalT-VIb gene was located to human chromosome 18q12.1 between markers WI-9180 and SGC35630 by radiation hybrid mapping. The genomic organization and adjacent gene content of g 4GalT-VIb were identified by comparing its cDNA sequence with three genomic sequences AC017100, AP002474 and AP001336, which showed that g 4GalT-VIb spans an ~58 u kb region and is composed of 8 exons. In addition, the most conserved motif composed of 41 residues, LXYX 3 FGGVSXL(T/S)X 2 QFX 2 INGFPNX(Y/F)WGWGGEDDDX 2 NR, was defined according to 17 sequences of g 4GalTs from seven different organisms for the first time.
{"title":"Molecular Cloning, Genomic Organization, and Mapping of β4GalT-VIb, a brain Abundant Member of β4-galactosyltransferase Gene Family, to Human Chromosome 18q12.1","authors":"Yuxin Fan, Long Yu, Q. Tu, Ruomu Gong, Ying Jiang, Qi Zhang, F. Dai, Chiyuan Chen, Shouyuan Zhao","doi":"10.1080/10425170290019838","DOIUrl":"https://doi.org/10.1080/10425170290019838","url":null,"abstract":"In the present study, a brain abundant member of g 4-galactosyltransferase gene family with an open reading frame encoding 343 amino acids was cloned and identified from a human leukemia cell cDNA library. The putative protein sequence is about 94.8 and 94.2% identical to the 382-amino-acid mouse and rat g 4-galactosyltransferase respectively and also contains cysteine residues previously shown to be important for the function of the gene family members. This cDNA (tentatively termed g 4GalT-VIb) is identical to a recently reported cDNA (tentatively termed g 4GalT-VIa) of human g 4-galactosyltransferase except lacking one exon, suggesting that these two cDNAs are two different alternative transcripts of the same gene. Northern hybridization showed that the new alternative transcript, g 4GalT-VIb, is expressed in all 16 human tissues tested with highest level in brain and rich level in testis, thymus and pancreas, whereas weak expression was detected in lung. The g 4GalT-VIb gene was located to human chromosome 18q12.1 between markers WI-9180 and SGC35630 by radiation hybrid mapping. The genomic organization and adjacent gene content of g 4GalT-VIb were identified by comparing its cDNA sequence with three genomic sequences AC017100, AP002474 and AP001336, which showed that g 4GalT-VIb spans an ~58 u kb region and is composed of 8 exons. In addition, the most conserved motif composed of 41 residues, LXYX 3 FGGVSXL(T/S)X 2 QFX 2 INGFPNX(Y/F)WGWGGEDDDX 2 NR, was defined according to 17 sequences of g 4GalTs from seven different organisms for the first time.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"57 1","pages":"1 - 8"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84064836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290019892
Elizabeth Barnes, J. Askham, Pamela F. Jones
The Smad family of proteins have been implicated as major components of the TGF g signalling pathway and are important mediators of its pleiotrophic effects. Here we describe the cloning and characterization of the mink ( Mustela vison ) ortholog of Smad4. Mink Smad4 has a high level of conservation to its human counterpart showing 96% homology at the DNA level and 99% at the amino acid level. This is in agreement with the close homologies seen for the rat and mouse orthologs. In vitro transcription and translation shows the expression of a protein of predicted molecular weight, of identical size to its human counterpart.
{"title":"cDNA Cloning and Molecular Characterization of Mink SMAD4","authors":"Elizabeth Barnes, J. Askham, Pamela F. Jones","doi":"10.1080/10425170290019892","DOIUrl":"https://doi.org/10.1080/10425170290019892","url":null,"abstract":"The Smad family of proteins have been implicated as major components of the TGF g signalling pathway and are important mediators of its pleiotrophic effects. Here we describe the cloning and characterization of the mink ( Mustela vison ) ortholog of Smad4. Mink Smad4 has a high level of conservation to its human counterpart showing 96% homology at the DNA level and 99% at the amino acid level. This is in agreement with the close homologies seen for the rat and mouse orthologs. In vitro transcription and translation shows the expression of a protein of predicted molecular weight, of identical size to its human counterpart.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"52 1","pages":"47 - 53"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82836459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290029990
A. Hill, N. Brown, M. S. Hill, D. Wells
The EXT family of genes is involved in the developmentally important biosynthesis of heparan sulfate molecules. Members of the EXT family have a demonstrated role in gastrulation, wing formation in flies, and proper bone development in vertebrates. EXT family members have been isolated from several phylogenetically diverse species. We report here, the isolation of the first Xenopus laevis EXT1 family member and discuss the evolutionary origins of this gene family.
{"title":"Identification of the Xenopus laevis cDNA for EXT1: A Phylogenetic Perspective","authors":"A. Hill, N. Brown, M. S. Hill, D. Wells","doi":"10.1080/10425170290029990","DOIUrl":"https://doi.org/10.1080/10425170290029990","url":null,"abstract":"The EXT family of genes is involved in the developmentally important biosynthesis of heparan sulfate molecules. Members of the EXT family have a demonstrated role in gastrulation, wing formation in flies, and proper bone development in vertebrates. EXT family members have been isolated from several phylogenetically diverse species. We report here, the isolation of the first Xenopus laevis EXT1 family member and discuss the evolutionary origins of this gene family.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"23 1","pages":"85 - 92"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90276643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290019883
J. Kitanaka, N. Kitanaka, M. Takemura, Xiao‐Bing Wang, C. Hembree, N. L. Goodman, G. Uhl
The expression of the heterotrimeric GTP-binding protein g 1 subunit gene ( GNB1 ) is regulated by psychostimulants such as cocaine and amphetamines. Since the up-regulation appears to be one of the candidate processes of sensitization, it is necessary to elucidate the cellular and molecular mechanism of the GNB1 gene regulation for a better understanding the establishment of sensitization. In the present study, we describe the isolation and nucleotide sequence analysis of the GNB1 gene promoter region. We have isolated approximately 10 u kb of the 5'-flanking region of the mouse of GNB1 gene and found potential elements involved in putative transcriptional control of the GNB1, such as AP1, AP2, Sp1, cyclic AMP response element, and nuclear factor s B recognition sites, within the sequences 0.3 u kb upstream from the putative transcription start site. This region was highly rich in G+C content, but lacked TATA or CATT boxes. Comparing the nucleotide sequence of the cDNA clone with the human genome databases using the blast program a region containing putative exon 1 and promoter of the human GNB1 gene in chromosome 1 was found. The cloning and sequence analysis of an extensive portion of the 5'-flanking regulatory region of the GNB1 gene provides new insights into the factors involved in the regulation by psychostimulants of GNB1 expression.
异三聚体gtp结合蛋白g1亚基基因(GNB1)的表达受可卡因和安非他明等精神兴奋剂的调控。由于上调可能是致敏的候选过程之一，因此有必要阐明GNB1基因调控的细胞和分子机制，以便更好地理解致敏的建立。在本研究中，我们描述了GNB1基因启动子区域的分离和核苷酸序列分析。我们在小鼠GNB1基因的5'侧区分离了大约10 u kb，并在推定的转录起始位点上游0.3 u kb的序列中发现了可能参与GNB1转录控制的潜在元件，如AP1、AP2、Sp1、环状AMP响应元件和核因子B识别位点。该地区G+C含量非常丰富，但缺乏TATA盒或CATT盒。利用blast程序将cDNA克隆的核苷酸序列与人类基因组数据库进行比较，发现1号染色体上含有假定的人类GNB1基因的外显子1和启动子区域。GNB1基因5'侧调控区域的大量克隆和序列分析为精神兴奋剂调节GNB1表达的相关因素提供了新的见解。
{"title":"Isolation and Sequencing of a Putative Promoter Region of the Murine G Protein β1 Subunit ( GNB1 ) Gene","authors":"J. Kitanaka, N. Kitanaka, M. Takemura, Xiao‐Bing Wang, C. Hembree, N. L. Goodman, G. Uhl","doi":"10.1080/10425170290019883","DOIUrl":"https://doi.org/10.1080/10425170290019883","url":null,"abstract":"The expression of the heterotrimeric GTP-binding protein g 1 subunit gene ( GNB1 ) is regulated by psychostimulants such as cocaine and amphetamines. Since the up-regulation appears to be one of the candidate processes of sensitization, it is necessary to elucidate the cellular and molecular mechanism of the GNB1 gene regulation for a better understanding the establishment of sensitization. In the present study, we describe the isolation and nucleotide sequence analysis of the GNB1 gene promoter region. We have isolated approximately 10 u kb of the 5'-flanking region of the mouse of GNB1 gene and found potential elements involved in putative transcriptional control of the GNB1, such as AP1, AP2, Sp1, cyclic AMP response element, and nuclear factor s B recognition sites, within the sequences 0.3 u kb upstream from the putative transcription start site. This region was highly rich in G+C content, but lacked TATA or CATT boxes. Comparing the nucleotide sequence of the cDNA clone with the human genome databases using the blast program a region containing putative exon 1 and promoter of the human GNB1 gene in chromosome 1 was found. The cloning and sequence analysis of an extensive portion of the 5'-flanking regulatory region of the GNB1 gene provides new insights into the factors involved in the regulation by psychostimulants of GNB1 expression.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"39 1","pages":"39 - 45"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85039292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290030060
Jiwang Chen, C. Tauer, Yinghua Huang
The 615-bp nucleotide sequences of the first partial internal transcribed spacer (ITS-1), 5.8S rDNA and ITS-2 region from Pinus taeda L. (loblolly pine) and Pinus echinata Mill. (shortleaf pine) are reported. The two pine species show the same nucleotide sequences in this region, which indicates their close phylogenetic relationship. However, our reported nucleotide sequence in this region from shortleaf pine is different from the previous report for shortleaf pine in GenBank (accession number: AF037016). Our PCR-RFLP analysis of this region confirms our sequencing data. This correction is important for pine phylogenetic studies because it is located in the conserved 5.8S rDNA region.
{"title":"Nucleotide Sequences of the Internal Transcribed Spacers and 5.8S Region of Nuclear Ribosomal DNA In Pinus taeda L. and Pinus echinata Mill.","authors":"Jiwang Chen, C. Tauer, Yinghua Huang","doi":"10.1080/10425170290030060","DOIUrl":"https://doi.org/10.1080/10425170290030060","url":null,"abstract":"The 615-bp nucleotide sequences of the first partial internal transcribed spacer (ITS-1), 5.8S rDNA and ITS-2 region from Pinus taeda L. (loblolly pine) and Pinus echinata Mill. (shortleaf pine) are reported. The two pine species show the same nucleotide sequences in this region, which indicates their close phylogenetic relationship. However, our reported nucleotide sequence in this region from shortleaf pine is different from the previous report for shortleaf pine in GenBank (accession number: AF037016). Our PCR-RFLP analysis of this region confirms our sequencing data. This correction is important for pine phylogenetic studies because it is located in the conserved 5.8S rDNA region.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"188 1","pages":"129 - 131"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83052689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290019847
R. Martínez-Arias, J. Bertranpetit, D. Comas
Variation analyses in the human genome at the sequence level, especially human genetic population analysis and genetic epidemiology, are hampered by the difficulty to ascertain haplotypes on autosomal regions. We have designed a new methodological approach to obtain autosomal haploid sequences from diploid organisms. First, genotypes are unambiguously determined through long-range PCR and diploid DNA sequencing. Second, cloning the whole PCR-amplified segment and sequencing a single clone for those fragments that presented a heterozygous position discern the allelic phase. The second allele is deduced from the genotype, and the phase reconfirmed by sequencing a second clone. A hundred human chromosomes were analysed for a 5.4 u kb encompassing the glucocerebrosidase pseudogene on human chromosome 1. Haplotypes were unambiguously ascertained for all samples. The manner to combine the used techniques makes this approach a novelty. Haploid sequences from diploid organisms are obtained in a less time consuming and more accurate manner than in other used procedures.
在序列水平上对人类基因组的变异分析，特别是人类遗传群体分析和遗传流行病学，由于难以确定常染色体区域的单倍型而受到阻碍。我们设计了一种新的方法从二倍体生物体中获得常染色体单倍体序列。首先，基因型是通过远程PCR和二倍体DNA测序确定的。其次，克隆整个pcr扩增片段，并对呈现杂合位置的片段进行单克隆测序，以确定等位基因期。第二个等位基因从基因型中推断出来，并通过对第二个克隆进行测序来重新确认阶段。对100条人类染色体进行了分析，发现人类1号染色体上含有5.4 u kb的糖脑苷酶假基因。所有样品的单倍型都得到了明确的确定。将所使用的技术结合起来的方式使这种方法具有新颖性。从二倍体生物体中获得单倍体序列，比其他使用的方法耗时更少，更准确。
{"title":"Determination of Haploid DNA Sequences in Humans: Application to the Glucocerebrosidase Pseudogene","authors":"R. Martínez-Arias, J. Bertranpetit, D. Comas","doi":"10.1080/10425170290019847","DOIUrl":"https://doi.org/10.1080/10425170290019847","url":null,"abstract":"Variation analyses in the human genome at the sequence level, especially human genetic population analysis and genetic epidemiology, are hampered by the difficulty to ascertain haplotypes on autosomal regions. We have designed a new methodological approach to obtain autosomal haploid sequences from diploid organisms. First, genotypes are unambiguously determined through long-range PCR and diploid DNA sequencing. Second, cloning the whole PCR-amplified segment and sequencing a single clone for those fragments that presented a heterozygous position discern the allelic phase. The second allele is deduced from the genotype, and the phase reconfirmed by sequencing a second clone. A hundred human chromosomes were analysed for a 5.4 u kb encompassing the glucocerebrosidase pseudogene on human chromosome 1. Haplotypes were unambiguously ascertained for all samples. The manner to combine the used techniques makes this approach a novelty. Haploid sequences from diploid organisms are obtained in a less time consuming and more accurate manner than in other used procedures.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"22 1","pages":"13 - 9"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75932658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Contamination in the Draft of the Human Genome Masquerades As Lateral Gene Transfer","authors":"E. Willerslev, T. Mourier, A. Hansen, B. Christensen, I. Barnes, S. Salzberg","doi":"10.1080/10425170290023392","DOIUrl":"https://doi.org/10.1080/10425170290023392","url":null,"abstract":"(2002). Contamination in the Draft of the Human Genome Masquerades As Lateral Gene Transfer. DNA Sequence: Vol. 13, No. 2, pp. 75-76.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"15 1","pages":"75 - 76"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88845610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290019874
P. Chimwamurombe, B. Wingfield, A. Botha, M. Wingfield
Cryphonectria cubensis causes a serious Eucalyptus canker disease. Fungal cell wall degrading enzymes (CWDEs) are important during the early stages of interaction of the fungus with Eucalyptus. To improve our understanding of the molecular regulation of the interaction of Eucalyptus and C. cubensis, the relevant genes involved in this interaction should be identified, cloned and studied. The aim of this study was, therefore, to clone the endopolygalacturonase (endoPG) gene of C. cubensis. C. cubensis was grown on a medium supplemented with Eucalyptus cell wall extracts. Degenerate primers were designed to amplify part of the endoPG gene from C. cubensis genomic DNA. The resulting sequence was used to design specific primers for use in inverse PCR to amplify the entire endoPG gene of C. cubensis ( ccen-1 ). The endoPG sequence of C. cubensis has 93% amino acid sequence similarity to that of the chestnut blight pathogen, Cryphonectria parasitica.
{"title":"Molecular Analysis of an Endopolygalacturonase Gene from a Eucalyptus Canker Pathogen, Cryphonectria cubensis","authors":"P. Chimwamurombe, B. Wingfield, A. Botha, M. Wingfield","doi":"10.1080/10425170290019874","DOIUrl":"https://doi.org/10.1080/10425170290019874","url":null,"abstract":"Cryphonectria cubensis causes a serious Eucalyptus canker disease. Fungal cell wall degrading enzymes (CWDEs) are important during the early stages of interaction of the fungus with Eucalyptus. To improve our understanding of the molecular regulation of the interaction of Eucalyptus and C. cubensis, the relevant genes involved in this interaction should be identified, cloned and studied. The aim of this study was, therefore, to clone the endopolygalacturonase (endoPG) gene of C. cubensis. C. cubensis was grown on a medium supplemented with Eucalyptus cell wall extracts. Degenerate primers were designed to amplify part of the endoPG gene from C. cubensis genomic DNA. The resulting sequence was used to design specific primers for use in inverse PCR to amplify the entire endoPG gene of C. cubensis ( ccen-1 ). The endoPG sequence of C. cubensis has 93% amino acid sequence similarity to that of the chestnut blight pathogen, Cryphonectria parasitica.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"43 1","pages":"33 - 37"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80819851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290029981
D. Bodenmiller, C. Baxter, David V. Hansen, S. Potter
Nine thousand and eighty-eight base pairs of the chicken Hoxa 11 gene, including 8470 bases 5' of the translation start site were sequenced, and the characteristics of the upstream sequence investigated. Consistent with previous findings that middle repetitive elements are rare in the HoxA cluster, no repetitive elements were found other than simple oligonucleotide repeats. Multiple and pairwise alignments of the chicken upstream sequence with its human and mouse orthologs revealed multiple regions of 80% or higher homology across species. For the chicken, these regions were separated by sequences with no significant homology to human, mouse, or in most cases any other Genbank sequences. Selective clustering of transcription factor binding motifs was found to occur within the conserved homologous regions, suggesting evolutionary conservation of critical regulatory sequences. Of particular interest, seven conserved Cdx binding sites were found in the Hoxa 11 promoter, suggesting regulation by a non-clustered Caudal homeobox gene. Previous analysis of the mouse and human Hoxa 11 genes found a conserved antisense transcript, of unknown function. The chicken Hoxa 11 antisense strand included a conserved open reading frame capable of encoding 168 amino acids. Comparison of this region in mouse and chicken showed seven insertion/deletions, with each a multiple of three bases, thereby preserving open reading frame.
{"title":"Phylogenetic Analysis of Hoxa 11 Sequences Reveals Absence of Transposable Elements, Conservation of Transcription Factor Binding Sites, and Suggests Antisense Coding Function","authors":"D. Bodenmiller, C. Baxter, David V. Hansen, S. Potter","doi":"10.1080/10425170290029981","DOIUrl":"https://doi.org/10.1080/10425170290029981","url":null,"abstract":"Nine thousand and eighty-eight base pairs of the chicken Hoxa 11 gene, including 8470 bases 5' of the translation start site were sequenced, and the characteristics of the upstream sequence investigated. Consistent with previous findings that middle repetitive elements are rare in the HoxA cluster, no repetitive elements were found other than simple oligonucleotide repeats. Multiple and pairwise alignments of the chicken upstream sequence with its human and mouse orthologs revealed multiple regions of 80% or higher homology across species. For the chicken, these regions were separated by sequences with no significant homology to human, mouse, or in most cases any other Genbank sequences. Selective clustering of transcription factor binding motifs was found to occur within the conserved homologous regions, suggesting evolutionary conservation of critical regulatory sequences. Of particular interest, seven conserved Cdx binding sites were found in the Hoxa 11 promoter, suggesting regulation by a non-clustered Caudal homeobox gene. Previous analysis of the mouse and human Hoxa 11 genes found a conserved antisense transcript, of unknown function. The chicken Hoxa 11 antisense strand included a conserved open reading frame capable of encoding 168 amino acids. Comparison of this region in mouse and chicken showed seven insertion/deletions, with each a multiple of three bases, thereby preserving open reading frame.","PeriodicalId":11381,"journal":{"name":"DNA Sequence","volume":"17 1","pages":"77 - 83"},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87409485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2002-01-01DOI: 10.1080/10425170290019919
F. Kugawa, Masatada Aoki
We previously cloned the cDNA of the transcription factor TFIIS (SII) from Xenopus laevis and showed that its expression was not constant during Xenopus development. To investigate its regulation, we cloned the genomic DNA of Xenopus TFIIS, focusing on the 5'-promoter region. Here, we present the Xenopus TFIIS genomic sequence ( m 1730 to +214) and transcription start site (cap site). We define the position of the primary cap site as the adenine located 142 u bp upstream from the adenine of the ATG (Met) codon. Another putative start-site region, where 13 transcriptional start sites are clustered within 12 u bp, was mapped about 100 u bp downstream of the primary cap site. Although a computer search found putative trans -element binding sites proximal to two Xenopus TFIIS transcription start sites, we could not identify typical "TATA" or "CAATT" boxes upstream of the primary cap site, probably owing to TFIIS's character as a "house keeping gene".
我们从非洲爪蟾中克隆了转录因子TFIIS (SII)的cDNA，发现其在爪蟾发育过程中的表达不是恒定的。为了研究其调控机制，我们克隆了非洲爪蟾TFIIS的基因组DNA，重点克隆了5'-启动子区域。在这里，我们展示了非洲爪蟾TFIIS基因组序列(m 1730至+214)和转录起始位点(cap位点)。我们将主要帽位的位置定义为位于ATG (Met)密码子腺嘌呤上游142 u bp的腺嘌呤。另一个假定的起始位点区域，其中13个转录起始位点聚集在12 u bp内，被定位在主帽位点下游约100 u bp处。尽管计算机搜索在两个爪鼠TFIIS转录起始位点附近发现了假定的反式元件结合位点，但我们无法在主要帽位上游找到典型的“TATA”或“CAATT”盒子，这可能是由于TFIIS作为“管家基因”的特性。
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