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At least 181 records · Page 10Linked to original sources
PubMed1995

The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana.

A new Arabidopsis thaliana (ecotype Columbia) genomic library has been constructed in Yeast Artificial Chromosomes: the CIC library (for CEPH, INRA and CNRS). Optimization of plant culture conditions and protoplast preparation allowed the recovery of large amounts of viable protoplasts. Mechanical shearing of DNA was minimized by isolation of DNA from protoplasts embedded in agarose. Cloning of large inserts was favored by including two successive size fractionation steps (after partial EcoRI digestion and after ligation with the vector arms), which selected DNA fragments larger than 350 kb. The library consists of 1152 clones with an average insert size of 420 kb. Clones carrying chloroplast DNA and various nuclear repeated sequences have been identified. Twenty-one per cent of the clones are found to contain chloroplast DNA. Therefore, the library represents around four nuclear genome equivalents. The clones containing 5S rDNA genes, 18S-25S rDNA sequences and the 180 bp paracentromeric repeated element account for 3.6%, 8.9% and 5.8%, respectively. Only one clone was found to carry the 160 bp paracentromeric repeated element. Given the smaller size of clones carrying Arabidopsis repeated DNA, the average size of remaining clones is around 480 kb. The library was screened by PCR amplification using pairs of primers corresponding to sequences dispersed in the genome. Seventy out of 76 pairs of primers identified from one to seven YAC clones. Thus at least 92% of the genome is represented in the CIC library. The survey of the library for clones containing unlinked DNA sequences indicates that the proportion of chimeric clones is lower than 10%.

Arabidopsis↗
PubMed2006

Construction and partial characterization of a Corynebacterium pseudotuberculosis bacterial artificial chromosome library through genomic survey sequencing.

Corynebacterium pseudotuberculosis is a gram-positive bacterium that causes caseous lymphadenitis in sheep and goats. However, despite the economic losses caused by caseous lymphadenitis, there is little information about the molecular mechanisms of pathogenesis of this bacterium. Genomic libraries constructed in bacterial artificial chromosome (BAC) vectors have become the method of choice for clone development in high-throughput genomic-sequencing projects. Large-insert DNA libraries are useful for isolation and characterization of important genomic regions and genes. In order to identify targets that might be useful for genome sequencing, we constructed a C. pseudotuberculosis BAC library in the vector pBeloBAC11. This library contains about 18,000 BAC clones, with inserts ranging in size from 25 to 120 kb, theoretically representing a 390-fold coverage of the C. pseudotuberculosis genome (estimated to be 2.5-3.1 Mb). Many genomic survey sequences (GSSs) with homology to C. diphtheriae, C. glutamicum, C. efficiens, and C. jeikeium proteins were observed within a sample of 215 sequenced clones, confirming their close phylogenetic relationship. Computer analyses of GSSs did not detect chimeric, deleted, or rearranged BAC clones, showing that this library has low redundancy. This GSSs collection is now available for further genetic and physical analysis of the C. pseudotuberculosis genome. The GSS strategy that we used to develop our library proved to be efficient for the identification of genes and will be an important tool for mapping, assembly, comparative, and functional genomic studies in a C. pseudotuberculosis genome sequencing project that will begin this year.

Chromosomes, Artificial, Bacterial↗
PubMed1994

Exon amplification from complete libraries of genomic DNA using a novel phage vector with automatic plasmid excision facility: application to the mouse neurofibromatosis-1 locus.

The identification of transcription units in the vicinity of chromosomal lesions found in tumours is an essential step in the identification of new oncogenes. Here, we describe a lambda phage vector system for genomic exon-trapping (lambda GET), which dramatically simplifies the task of exon amplification from genomic DNA. The vector accommodates about 6.5 to 19 kb of DNA and allows inserts to be automatically subcloned as multi-copy plasmids containing splice donor and acceptor sites positioned flanking the inserted genomic DNA. RNA transcripts derived from such plasmids are processed in vivo and exons contained within the inserted genomic fragments become flanked by known sequences in the resulting mRNAs. RNA-based PCR can then be used for subsequent cloning and sequence analysis of trapped exons. We have exploited the large cloning capacity of lambda GET to construct highly redundant complete genomic libraries from Sau3AI partially digested vertebrae DNAs. Using this system, we have analysed a region of about 1 MB around the mouse neurofibromatosis-1 locus and have identified novel transcription units flanking the Nf-1 gene.

Amino Acid Sequence↗
PubMed1986

Factors which equalize the representation of genome segments in recombinant libraries.

Genomic segments which contain inverted repetitions longer than 300 bp are frequently lost from recombinant libraries grown on rec+ hosts. We have found that 9% of phage lambda clones that contain 15-20-kb insertions of human or Drosophila DNA are inhibited on rec+ hosts and as a result will become under-represented in amplified genomic libraries. We have therefore examined several factors of both host and vector origin which affect the fidelity of representation of genomic sequences in recombinant DNA libraries constructed in bacteriophage lambda vectors. This loss may be diminished if the vector carries either a chi element or a functional gam gene. The most successful approach, however, involves using a host with mutations in recB, recC, and sbcB, or in recD. We have shown that recombinant clones which require such mutant hosts for growth are somewhat more likely to contain DNA derived from loci in the genome which are polymorphic than are clones recovered on conventional hosts.

Animals↗
PubMed1998

The genomic and sequence analysis of rat histone H2B genes.

In addition to previously characterized testis-specific and somatic H2B histone genes, two somatic histone H2B genes, hereafter called sH2B-2 and sH2B-3, were isolated from a rat genomic library, genomic organization was determined, and their promoter was sequenced. Like many other H2B genes, sH2B-2 gene was closely linked to H2A gene whereas H3 gene was located upstream of sH2B-3 gene. Deletion and mutation analysis of 5' sequence fused to CAT reporter gene revealed that the interaction between CCAAT and octamer binding factors is important for S-phase-specific activation of sH2B-3 gene.

3T3 Cells↗
PubMed2006

Using partial genomic fosmid libraries for sequencing complete organellar genomes.

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However; for some organisms, it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

DNA↗
PubMed2000

Onchocerca volvulus superoxide dismutase genes: identification of functional promoters for pre-mRNA transcripts which undergo trans-splicing.

The genes encoding three forms of superoxide dismutase, the cytosolic and extracellular CuZn superoxide dismutases and the mitochondrial Mn superoxide dismutase, were isolated from an Onchocerca volvulus lambda fix II genomic library. Genomic Southern blot analyses indicate single-copy genes in the O. volvulus genome. The O. volvulus cytosolic and extracellular CuZnSOD genes (Ov-sod-1 and Ov-sod-2) are separated by 0.8 kb of sequence and are convergently transcribed. Since the transcripts from all three sod genes are trans-spliced, the transcription start point of each gene was determined in a heterologous system that lacks trans-splicing machinery by in vitro transcription using Drosophila embryo nuclear extracts, followed by primer extension experiments. The ability of the 5' flanking region of the genes encoding the three Ov-SODs to promote transcription was further examined in transient transfections of Chinese hamster ovary cells. In firefly luciferase reporter assays, the Ov-sod-1 and -2 and the MnSOD (Ov-sod-3) gene promoters showed minimal, strong, and moderate levels of activity in these cells, respectively. Both Ov-sod-2 and -3 gene promoter regions showed an initial increase in activity in response to 5' deletions. The results from the in vitro transcription experiments and the luciferase reporter assays were consistent and suggest the presence of Inr-like elements in the promoter regions of the Ov-sod genes.

Animals↗
PubMed1996

[Construction of Chinese genomic cosmid library].

A Chinese genomic library has been constructed using SuperCos1 cosmid vector. 6.09 x 10(5) clones were obtained with an everage insert size of 40 kb ranging from 32 to 45 kb, which cover approximately 8.12 fold human genomic DNA. DNA pools prepared from the total library were screened with 6 known markers distributed on different chromosomes, which all were tested positive.

Asian People↗
PubMed1995

Human androgen-induced growth factor in prostate and breast cancer cells: its molecular cloning and growth properties.

Androgen-induced growth factor (AIGF) has hormone-regulated properties in the mouse Shionogi carcinoma cell line. To investigate whether or not it is involved in growth of human hormone-responsive cancers, we isolated the human AIGF gene from a placental genomic library. Genomic analyses suggested that the AIGF gene was about 6.5 kilobases in length containing five exons. The deduced amino acid sequence of human AIGF was completely identical with that of the mouse. RT-PCR analyses showed that prostate and breast cancer cell lines, LNCaP, PC-3, and MCF-7, slightly expressed the AIGF gene. Recombinant AIGF enhanced the growth of the human prostate cancer LNCaP cells, and it also markedly stimulated the growth of fibroblasts. These in vitro findings suggest that AIGF might be a possible autocrine or paracrine factor in hormone-responsive cancers.

3T3 Cells↗
PubMed1998

Molecular cloning, characterization, and expression of the chicken heme oxygenase-1 gene in transfected primary cultures of chick embryo liver cells.

Using chick heme oxygenase-1 (cHO-1) cDNA as a probe, three independent clones were identified from screening a lambda FixII chick genomic library. Genomic Southern blots using this cDNA probe or a cHO-1 5' specific probe showed that cHO-1 is a single-copy gene. Based on restriction enzyme analysis, Southern blots, polymerase chain reaction analysis and DNA sequencing, it was confirmed that the three overlapping clones isolated cover the entire cHO-1 gene, as well as approximately 10 kb of the flanking regions on both ends. As with mammalian HO-1x, cHO-1 has five exons and four introns. Computer analysis of the DNA sequence obtained identified consensus sequences corresponding to numerous transcription factor recognition elements. These include AP-1, AP-2, NF-kB, C/EBP, c-Myc and a metal-responding element identified in the promoter region, and two Sp-1 elements in intron 1. Transient expression studies in transfected primary cultures of chick embryo liver cells showed that a CAT reporter gene construct containing 2.8 kb of the cHO-1 promoter region responded to sodium arsenite, H2O2, transition metals and 12-0-tetradecanoylphorbol 13-acetate, but not to heme. Studies with deletion mutants, consisting of various lengths of the cHO-1 promoter region, indicated that there are two regions important for sodium arsenite induction, one located between residues -1642 and -1293, and the second located in the first 263 base pairs of the cHO-1 promoter. DNA binding studies by electrophoretic mobility shift assay showed that nuclear protein isolated from primary cultures of chick embryo liver cells bound to the oligonucleotide probe containing an AP-1 element identified at -1573 to -1580. In addition, such binding was increased by cobalt or sodium arsenite treatment.

Animals↗
PubMed1991

Transient occurrence of extrachromosomal DNA of an Arabidopsis thaliana transposon-like element, Tat1.

Analysis of 11 genomic clones containing the S-adenosylmethionine synthetase 1 gene (sam1) of Arabidopsis thaliana revealed the presence of a 431-base-pair (bp) insertion in the 3' end of sam1 in one of these clones. The inserted sequence, called Tat1, shows structural features of a transposon. It is flanked by a 5-bp duplication of the target site DNA and has 13-bp inverted repeats at its termini. Two highly homologous elements situated in a different genomic context were isolated from a genomic library. Genomic Southern analysis indicates that there are at least four copies of Tat1 present in the A. thaliana ecotype Columbia genome. Different hybridization patterns are observed with DNAs derived from different ecotypes of Arabidopsis thaliana, indicating that the element has moved since the divergence of these ecotypes. In two populations of A. thaliana, linear extrachromosomal Tat1-homologous DNA has been observed. The presented data are consistent with the hypothesis that Tat1 is an active transposable element.

Base Sequence↗
PubMedDate not supplied

Identification of (CA/GT)n polymorphisms within the X-linked chronic granulomatous disease (X-CGD) gene: utility for prenatal diagnosis.

PURPOSE: The majority of known female carriers of X-linked chronic granulomatous disease (X-CGD), a deficiency of the gp91-phox (phagocyte oxidase) subunit and the most common genetic subtype of CGD, are not informative for the linked restriction fragment length polymorphisms (RFLPs) described to date. The isolation and characterization of two polymorphic (CA/GT)n repeats that lie within the X-CGD gene are reported, which are a useful linked marker for prenatal diagnosis. PATIENTS AND METHODS: cDNA for gp91-phox was used to probe a genomic library. Genomic clones were isolated and screened for (CA/GT)n repeats. The repeats were isolated and sequences surrounding the repeats were determined. Oligonucleotide primer pairs surrounding the repeats were chosen to facilitate polymerase chain reaction (PCR) across the repeat. RESULTS: Analysis of DNA derived from over 100 individuals shows both markers to be highly polymorphic with a resultant high proportion of heterozygosity in females. Several kindreds affected by X-CGD were studied and the (CA/GT)n length polymorphisms were shown to segregate with the clinical syndrome or biochemical carrier status. The technique was prospectively applied to several kindreds containing a carrier mother and an affected child. In a case where a male fetus was shown to carry the unaffected allele, the pregnancy was carried to term and the child was not affected. CONCLUSIONS: This approach is highly informative in a multiple allele system, can provide a technical analysis in just hours, requires only a ng of DNA, and permits the transport of diagnostic samples. Therefore, this method can be used early in pregnancy on a chorionic villus biopsy sample for prenatal diagnosis.

Alleles↗