It is clear that the construction of large insert DNA libraries is important for map-based gene cloning, the assembly of physical maps, and simple screening for specific genomic sequences. The bacterial artificial chromosome (BAC) system is likely to be an important tool for map-based cloning of genes since BAC libraries can be constructed simply and analyzed more efficiently than yeast artificial chromosome (YAC) libraries. BACs have significantly expanded the size of fragments from eukaryotic genomes that can be cloned in Escherichia coli as plasmid molecules. To facilitate the isolation of molecular-biologically important genes in Ashbya gossypii, we constructed Ashbya chromosome-specific BAC libraries using pBeloBAC11 and pBACwich vectors with an average insert size of 100 kb, which is equivalent to 19.8X genomic coverage. pBACwich was developed to streamline map-based cloning by providing a tool to integrate large DNA fragments into specific sites in chromosomes. These chromosome-specific libraries have provided a useful tool for the further characterization of the Ashbya genome including positional cloning and genome sequencing.
Ascomycota* ; Chromosomes, Artificial, Bacterial ; Chromosomes, Artificial, Yeast ; Clone Cells ; Cloning, Organism ; DNA ; Escherichia coli ; Gene Library ; Genome ; Mass Screening ; Plasmids

OBJECTIVETo annotate the human genome 3p24-p25 478 kb complete sequence.

METHODSThe protein-coding genes in the genomic sequence were identified by using ab initio gene finding, homology-based similarity database searching and all or partial mRNA aligning with genomic sequence, and the content feature of the genomic sequence were analyzed by using EMBOSS package.

RESULTSTwo known genes SLC6A1 and SLC6A11 were identified; as well as the GC content of this genomic sequence was 47% and 3 putative CpG islands were predicted in the genomic sequence, located in 130,685-131,516 bp, 307,090-307,870 bp and 415,585-416,308 bp, respectively.

CONCLUSIONSThe methods, as mentioned above, might be used for annotating the biological information in the genomic sequence, such as gene structure, GC content, CpG island.

Base Sequence ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 3 ; Genome, Human ; Human Genome Project ; Humans ; Molecular Sequence Data

PURPOSE: Williams syndrome is characterized by supravalvular aortic stenosis, mental retardation and peculiar facial appearance. Its genetic etiology is considered to be a hemizygotic deletion in Chromosome 7q11.23, which includes the elastin gene. We examined the hemizygotic deletion of Chromosome 7q11.23 in 12 Korean Williams syndrome patients and 8 patients with isolated supravalvular aortic stenosis and performed deletion mapping in the Williams syndrome patients. METHODS: Hemizygotic deletion was determined with fluorescence in situ hybridization(FISH) using the bacterial artificial chromosome clone 244H3, which has the genomic DNA sequence of elastin gene, as a probe. For the deletion mapping, polymorphism analysis of 10 Williams syndrome patients and their parents was done with 9 dinucleotide repeat sequence polymorphic markers(D7S499, D7S672, D7S653, ELN, D7S2472, D7S1870, D7S2518, D7S675 and D7S669). RESULTS: In the Williams syndrome patients, FISH showed deletion in all. In patients with isolated supravalvular aortic stenosis, FISH showed deletion in one, partial deletion in another and no deletion in the other six patients. Polymorphism analysis showed that alleles at three loci(ELN, D7S2472 and D7S1870) were commonly deleted in the Williams syndrome patients. Paternal alleles were deleted in six patients and maternal alleles were deleted in four. CONCLUSION: Hemizygotic deletion could be detected in Williams syndrome patients with FISH and the commonly deleted loci were ELN, D7S2472 and D7S1870. Most patients with isolated supravalvular aortic stenosis showed no deletion with FISH and the genetic defect should be much smaller than what FISH could detect.
Alleles ; Aortic Stenosis, Supravalvular* ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 7* ; Clone Cells ; Dinucleotide Repeats ; Elastin ; Fluorescence ; Genes, vif ; Humans ; Intellectual Disability ; Parents ; Williams Syndrome*

PURPOSE: Williams syndrome is characterized by supravalvular aortic stenosis, mental retardation and peculiar facial appearance. Its genetic etiology is considered to be a hemizygotic deletion in Chromosome 7q11.23, which includes the elastin gene. We examined the hemizygotic deletion of Chromosome 7q11.23 in 12 Korean Williams syndrome patients and 8 patients with isolated supravalvular aortic stenosis and performed deletion mapping in the Williams syndrome patients. METHODS: Hemizygotic deletion was determined with fluorescence in situ hybridization(FISH) using the bacterial artificial chromosome clone 244H3, which has the genomic DNA sequence of elastin gene, as a probe. For the deletion mapping, polymorphism analysis of 10 Williams syndrome patients and their parents was done with 9 dinucleotide repeat sequence polymorphic markers(D7S499, D7S672, D7S653, ELN, D7S2472, D7S1870, D7S2518, D7S675 and D7S669). RESULTS: In the Williams syndrome patients, FISH showed deletion in all. In patients with isolated supravalvular aortic stenosis, FISH showed deletion in one, partial deletion in another and no deletion in the other six patients. Polymorphism analysis showed that alleles at three loci(ELN, D7S2472 and D7S1870) were commonly deleted in the Williams syndrome patients. Paternal alleles were deleted in six patients and maternal alleles were deleted in four. CONCLUSION: Hemizygotic deletion could be detected in Williams syndrome patients with FISH and the commonly deleted loci were ELN, D7S2472 and D7S1870. Most patients with isolated supravalvular aortic stenosis showed no deletion with FISH and the genetic defect should be much smaller than what FISH could detect.
Alleles ; Aortic Stenosis, Supravalvular* ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 7* ; Clone Cells ; Dinucleotide Repeats ; Elastin ; Fluorescence ; Genes, vif ; Humans ; Intellectual Disability ; Parents ; Williams Syndrome*

BACKGROUND: Williams syndrome is characterized by supravalvular aortic stenosis, mental retardation and peculiar facial appearance. Its genetic etiology is considered to be hemizygotic deletion in Chromosome 7q11.23 which includes the elastin gene. We examined the deletion in Korean Williams syndrome patients and their parents. MATERIALS AND METHOD: Sixteen patients were selected through careful clinical examination including echocardiography and cardiac angiography. Hemizygotic deletion of elastin gene was determined in patients and 21 parents with fluorescent in situ hybridization (FISH) technique using the bacterial artificial chromosome clone 244H3 probe or commercial WSCR probe. RESULTS: FISH showed hemizygotic deletion of chromosome 7 in all sixteen patients but none of their parents showed deletion. CONCLUSION: Hemizygotic deletion of elastin gene can be determined by FISH with new probe 244H3 in clinically suspected Williams syndrome patients.
Angiography ; Aortic Stenosis, Supravalvular ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 7 ; Clone Cells ; Echocardiography ; Elastin* ; Humans ; In Situ Hybridization, Fluorescence* ; Intellectual Disability ; Parents ; Williams Syndrome*

OBJECTIVETo determine the origin of a supernumerary small marker chromosome found in a fetus using prenatal BACs-on-Beads (BoBs) and single nucleotide polymorphism array (SNP-array) assays.

METHODSThe fetal sample was subjected to chromosomal karyotyping and BoBs analysis, and the results were validated with genome-wide scanning using a SNP microarray.

RESULTSThe fetus was found to have a 47,XX,+mar karyotype. BoBs analysis indicated that there was an amplification between 18p11.32 and 18p11.21, which was verified by the SNP-array assay as a 18.3 Mb duplication occurring at 18p11.32q11.1.

CONCLUSIONThe karyotype of the fetus was determined as 47,XX,+der18(18p11.32?18q11.1::18q11.1?18p11.32). The duplication has involved important genes including SMCHD1, LPIN2 and TGIF1, which may result in severe malformations in the fetus.

Adult ; Aneuploidy ; Chromosomes, Artificial, Bacterial ; genetics ; Chromosomes, Human, Pair 18 ; genetics ; Female ; Humans ; Karyotyping ; Microarray Analysis ; methods ; Polymorphism, Single Nucleotide ; Pregnancy ; Prenatal Diagnosis ; methods

To construct the plasmid of BAC-HSV-1 with GFP reporter gene and research the biological property of its infectious progeny virus. We constructed the plasmid C223-UL43-left-arms-UL47-right-arms which carried the homologous sequences of HSV-1. Liposome embedding method was used to transfect HSV-1 genome and the plasmid C223-UL43-left-arms-UL47-right-arms linearized by Mlu I digestion into Vero cells. After the successful homologous recombination in the eukaryotic cells, the recombinant BAC-HSV-1 with GFP reporter gene was generated. Then, the positive CPE were taken by plaque purification and by hirt extraction during the moment of the circularization of HSV-1 DNA, and the plasmid of BAC -HSV-1 was acquired. Electroporation was used to transfect the BAC -HSV-1 into DH10B, and then the single colonies of interest were confirmed both by MluI digestion and PCR. Experimental group and the control group cells were given BAC-HSV-1 plasmid and HSV-1 genomic DNA respectively to produce the BAC-HSV-1 and HSV-1 progeny virions. Vero cells were inoculated with the progeny virions at MOI = 0.1 and then a TCID50 assay was performed to determine the titers of virons in the two groups at 48 hours post inoculation. The plasmid BAC-HSV-1 was successfully constructed by the restriction enzyme analysis and the PCR. The titers of progeny virions were calculated by the TCID50 assay. No significant difference in the titers of virions between two groups was observed (P > 0.05). The infectious BAC-HSV-1 shuttle virus/plasmid between eukaryotic and prokaryotic cells was successfully constructed.
Animals ; Cercopithecus aethiops ; Chromosomes, Artificial, Bacterial ; Green Fluorescent Proteins ; genetics ; Herpesvirus 1, Human ; genetics ; pathogenicity ; Recombination, Genetic ; Vero Cells

OBJECTIVETo establish chromosome conformation capture (3C) strategy and to use this method for exploring the effect of chromosome conformation on human alpha-globin gene expression in the human alpha-globin transgenic mouse.

METHODSHomozygous human alpha-globin transgenic male mouse was crossed with KM female mouse. The 14.5-day post-coitum (dpc) embryos were used for the isolation of fetal liver and fetal brain cells. Homogeneous single-cell suspension was treated with formaldehyde to crosslink the chromatin conformation in the nuclear. The cross-linked chromatin compound was digested with Nco I and then ligated with T4 DNA ligase. The ligated compound was reversely cross-linked and then the ligated genomic DNA was purified for PCR analysis. The primers were designed along the two sides of cut and ligated sites. Semi-quantitative PCR was used to analyze the chromosome conformation of the whole human alpha-globin gene locus in fetal liver and fetal brain cells.

RESULTSWhen HS40 fragment was used as the fixed fragment, in fetal brain cells, the ligation frequencies of HS40 fragment with other fragments were decreased as the linear distances to HS40 fragment were increasing; while in fetal liver cells, two active genes (alpha1 and alpha2) fragments showed higher ligation frequencies with HS40 fragment than other fragments. However, the fragment containing an inactive gene (xi) displayed the comparable low ligation frequency as that in fetal brain. When alpha2 fragment was used as the fixed fragment, similarly, in fetal brain cells the ligation frequencies of alpha2 fragment with other ones were decreased as the linear distances increasing; when in fetal liver cells, it showed higher ligation frequencies with two upstream regulatory elements (HS 40 and 33). However, it showed a little bit lower ligation frequency with another two upstream regulatory elements (HS10 and 8) than those in fetal brain.

CONCLUSIONIn fetal liver cells, the distant regulatory elements are in close proximity to the downstream of the expressed globin genes through looping out, the interval region; however, in fetal brain, they were not in vicinity to the expressed globin genes.

Animals ; Brain ; metabolism ; Chromosomes, Artificial, Bacterial ; Chromosomes, Mammalian ; chemistry ; Female ; Gene Expression Regulation ; Humans ; Liver ; metabolism ; Male ; Mice ; Mice, Transgenic ; Nucleic Acid Conformation ; Regulatory Sequences, Nucleic Acid ; alpha-Globins ; biosynthesis ; genetics

EphA/ephrin-A mediated signaling has emerged as a key mechanism regulating axon guidance and topographic mapping, particularly in the well-characterized visual system from the retina to the superior colliculus (SC). In this study, EphA8 bacterial artificial chromosome (BAC) was manipulated to contain a floxed eGFP and human ephrin-A5 expression cassette using homologous recombination method. In the mice containing the recombinant BAC, it was shown that GFP is expressed in an anterior>posterior gradient in the SC. Furthermore, when these mice were crossed with the transgenic mice expressing Cre under the EphA8 promoter, it was evident that a GFP expression cassette was eliminated, and that human ephrin-A5 was ectopically expressed in the anterior region of the SC. This transgenic model would be useful to analyze the role of ephrin-A5 in the SC during the retinocollicular topography formation.
Animals ; Axons ; Chromosomes, Artificial, Bacterial ; Ephrin-A5 ; Homologous Recombination ; Humans ; Mice ; Mice, Transgenic ; Retina ; Superior Colliculi

To rapidly and accurately manipulate genome such as gene deletion, insertion and site mutation, the whole genome of a very virulent strain Md5 of Marek's disease virus (MDV) was inserted into bacterial artificial chromosome (BAC) through homogeneous recombination. The recombinant DNA was electroporated into DH10B competent cells and identified by PCR and restriction fragment length polymorphism analysis. An infectious clone of Md5BAC was obtained following transfection into chicken embryo fibroblast (CEF) cells. Furthermore, a lorf10 deletion mutant was constructed by two step Red-mediated homologous recombination. To confirm the specific role of gene deletion, the lorf10 was reinserted into the original site of MDV genome to make a revertant strain. All the constructs were rescued by transfection into CEF cells, respectively. The successful packaging of recombinant viruses was confirmed by indirect immunofluorescence assay. The results of growth kinetics assay and plaques area measurement showed that the lorf10 is dispensable for MDV propagation in vitro. Overall, this study successfully constructed an infectious BAC clone of MDV and demonstrated its application in genome manipulation; the knowledge gained from our study could be further applied to other hepesviruses.
Animals ; Chick Embryo ; Chickens ; Chromosomes, Artificial, Bacterial ; DNA, Recombinant ; Herpesvirus 2, Gallid/genetics* ; Marek Disease