Construction of a bacterial artificial chromosome library containing large Eco RI and Hin dIII genomic fragments of lettuce

Frijters, A.; Zhang, Z.; Damme, Mireille van; Wang, G. L.; Ronald, Pamela C.; Michelmore, Richard W.

doi:10.1007/s001220050428

Cited by 111 publications

(63 citation statements)

References 47 publications

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“…Tumor suppressor FAT gene mutation in oral cancer K Nakaya et al (Frijters et al, 1997) was digested with HindIII, and sizeselected HindIII-digested pooled male DNAs were used to generate a BAC library. These vectors were then transformed into and grown in Escherichia coli DH10B strain.…”

Section: Construction Of Bac Librarymentioning

confidence: 99%

Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array

Nakaya

Arita

et al. 2007

Oncogene

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Homozygous deletions (HD) provide an important resource for identifying the location of candidate tumor suppressor genes. To identify the tumor suppressor gene in oral cancer, we employed high-resolution comparative genomic hybridization (CGH)-array analysis. We identified a homozygous loss of FAT (4q35), a new member of the human cadherin superfamily, from genome-wide screening of copy number alterations in one primary oral cancer. This result was evaluated by genomic polymerase chain reaction in 13 oral cancer cell lines and 20 primary oral cancers and Southern blot in the cell lines. We found frequent exonic HD of FAT in the cell lines (3/13, 23%) and in primary oral cancers (16/20, 80%). FAT expression was absent in these cell lines. Homozygous deletion hot spots were observed in exon 1 (9/20, 45%) and exon 4 (7/20, 35%). Moreover, loss of gene expression was identified in other types of squamous cell carcinoma. The methylation status of the FAT CpG island in squamous cell carcinomas correlated negatively with its expression. Our results identify mutations in FAT as an important factor in the development of oral cancer and indicate the importance of FATs function in some squamous cell carcinomas.

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Section: Construction Of Bac Librarymentioning

confidence: 99%

Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array

Nakaya

Arita

et al. 2007

Oncogene

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“…com) to give an average genomic coverage of 2 Mb resolutions. 20 All of the clones were two endsequenced using Applied Biosystems 3700 sequencers (Foster City, CA, USA) and their sequences were BLAST-searched and mapped according to their positions in the University of California, Santa Cruz (UCSC) human genome database (http:// www.genome.ucsc.edu). Confirmation of the locus specificity of the chosen clones was performed by removing multiple loci-binding clones and individually examining them under standard fluorescence in situ hybridization (FISH), as described previously.…”

Section: Array Cghmentioning

confidence: 99%

Clinicopathological features and global genomic copy number alterations of pilomyxoid astrocytoma in the hypothalamus/optic pathway: comparative analysis with pilocytic astrocytoma using array-based comparative genomic hybridization

et al. 2008

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Pilomyxoid astrocytoma is a recently identified variant of pilocytic astrocytoma. We studied 11 circumscribed astrocytomas with focal (n ¼ 5) or diffuse (n ¼ 6) pilomyxoid features and compared them with 17 pilocytic astrocytomas from the hypothalamic/chiasmatic region in children. In one patient, a tumor that recurred after initial surgery had changed from pure-form pilomyxoid astrocytoma to the mixed form. The presence of a pilomyxoid area was associated with shorter survival. Next, we compared the comprehensive genome copy number changes in the pilomyxoid astrocytoma (n ¼ 4) with those in pilocytic astrocytoma (n ¼ 6) cases by array-based comparative genomic hybridization. The number of lost clones was larger in pilomyxoid astrocytoma than in pilocytic astrocytoma. Clones located in chromosome 8q24.3 were frequently gained in pilocytic astrocytoma (four of six) and in pilomyxoid astrocytoma (one of four). Clones located in 9p24.3 and 15q26.3 were lost in all of the pilomyxoid astrocytomas and in five of the pilocytic astrocytomas. Those in 8p23.3 showed a copy number loss in three of the pilomyxoid astrocytomas and four of the pilocytic astrocytomas. The frequency of copy number changes was significantly different between pilomyxoid astrocytoma and pilocytic astrocytoma in 47 (3.6%) clones, 20 of them having been located in 2p, 10 in 2q, and 11 in 3q. An unsupervised hierarchical clustering analysis classified the cases into three clusters: one pilomyxoid astrocytoma patient into one cluster, two pilomyxoid astrocytoma patients into another cluster, and six pilocytic astrocytoma patients and one pilomyxoid astrocytoma patient into the third cluster. In conclusion, the presence of mixed-form pilomyxoid astrocytoma, the acquisition of pilocytic astrocytoma features in a recurrent tumor in pure-form pilomyxoid astrocytoma, and the above results of the genome-wide gene copy number analysis suggest that pilomyxoid astrocytoma might be a pathologically and genetically related, aggressive variant of pilocytic astrocytoma with partially different genetic alterations.

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“…A sufficient amount of DNA is needed to compensate for the lower transformation efficiency of the large inserts (Frijters et al 1997;Leonardo and Sedivy 1990;Sheng et al 1995). However, overloading the pulse field gel to increase the amount of partially digested DNA can result in an undesirable quantity of small size DNA fragments trapped within the large fragments (Frijters et al 1997;Woo et al 1994). To avoid this problem, a ramped pulse (1-40 s) was used in the first size selection followed by a standard second size selection.…”

Section: Crucial Steps In the Construction Of The Librarymentioning

confidence: 99%

Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat

Lijavetzky

Muzzi

Wicker³

et al. 1999

Genome

117

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A genomic bacterial artificial chromosome (BAC) library of the A genome of wheat has been constructed. Triticum monococcum accession DV92 was selected for this purpose because it is a cultivated diploid wheat and one of the parental lines used in the construction of a saturated genetic map. Leaves from this accession were used to isolate high-molecular-weight DNA from nuclei. This DNA was partially digested with restriction enzyme Hind III, subjected to double size selection, electroeluted and cloned into the pINDIGO451 BAC vector. The library consists of 276 480 clones with an average insert size of 115 kb. Excluding the 1.33% of empty clones and 0.14% of clones with chloroplast DNA, the coverage of this library is 5.6 genome equivalents. With this genome coverage the probability of having any DNA sequence represented in this library is higher than 99.6%. Clones were sorted in 720 384-well plates and blotted onto 15 high-density filters. High-density filters were screened with several single or low-copy clones and five positive BAC clones were selected for further analysis. Since most of the T. monococcum BAC ends included repetitive sequences, a modification was introduced into the classical end-isolation procedure to select low copy sequences for chromosome walking.Key words: bacterial artificial chromosome, BAC library, Triticum monococcum, wheat.Résumé : Une banque génomique du génome A du blé a été produite dans des chromosomes bactériens artificiels (BAC). L'accession DV92 du Triticum monococcum a été choisie pour ces fins car il s'agit d'une lignée diploïde qui est cultivée et d'un des parents employés dans la construction de cartes génétiques saturées. De l'ADN de grand poids moléculaire a été extrait de noyaux des feuilles de ce génotype. Cet ADN a été partiellement digéré avec l'enzyme de restriction HindIII, assujetti à une double sélection en fonction de la taille, électroélué et cloné dans le vecteur BAC pINDIGO451. La banque comprend 276,480 clones dont les inserts ont une taille moyenne de 115 kb. En excluant 1,33 % de clones vides et 0,14 % de clones contenant de l'ADN chloroplastique, cette banque offre une couverture génomique équivalent à 5,6 génomes. Avec une telle couverture, la probabilité qu'une séquence y soit représentée excède 99,6 %. Les clones ont été disposés dans 720 boîtes à 384 puits et placés sur 15 membranes à haute densité. Ces membranes ont été criblées avec des clones à copie unique ou à faible nombre de copies et cinq clones BAC ont été choisis pour des analyses détaillées. Comme la plupart des extrémités de BAC du T. monococcum comprennent de l'ADN répété, une modification a été apportée à la méthode classique d'isolement des séquences terminales afin de sélectionner des séquences à faible nombre de copies pour les fins de marche chromosomique.

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Construction of a bacterial artificial chromosome library containing large Eco RI and Hin dIII genomic fragments of lettuce

Cited by 111 publications

References 47 publications

Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array

Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array

Clinicopathological features and global genomic copy number alterations of pilomyxoid astrocytoma in the hypothalamus/optic pathway: comparative analysis with pilocytic astrocytoma using array-based comparative genomic hybridization

Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat

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