Construction and Characterization of Human Chromosome 2-Specific Cosmid, Fosmid, and PAC Clone Libraries

Gingrich, Jeffrey C.; Boehrer, Denise M.; Garnes, Jeffrey; Johnson, Wanda; Wong, Benjamin S.; Bergmann, Anne; Eveleth, Gerald G.; Langlois, Richard G.; Carrano, A.V.

doi:10.1006/geno.1996.0077

Cited by 25 publications

(12 citation statements)

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“…BAC clones were identified using BLAST and the NCBI GenBank database. YAC clones were identified from the CEPH megaYAC library (27), and PAC and Fosmid clones were identified from the human chromosome 2-specific filter libraries LL02NP04 and LL02NC03 (26), respectively, using [ 32 P]-labeled DNA probes. These DNA probes were generated from PCR products using the Megaprime DNA labeling system, according to the manufacturer's recommendations (Amersham Biosciences UK Ltd.).…”

Section: Methodsmentioning

confidence: 99%

“…The ISPs (ISP1 and ISP2) were utilized to generate a 1,181-bp PCR product (Figure 3) that was radiolabeled and used to screen chromosome 2-specific P1-derived artificial chromosome (PAC) (LL02NP04) and Fosmid (LL02NC03) libraries (26) and the Centre d'Études du Polymorphisme Humain (CEPH) megaYAC library (27). This yielded 1 positive fosmid clone, AG63A8, and 1 nonchimeric yeast artificial chromosome (YAC) clone, 972C12.…”

Section: Figurementioning

confidence: 99%

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An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism

Bowl¹,

Nesbit²,

Harding³

et al. 2005

J. Clin. Invest.

135

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Section: Methodsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism

Bowl¹,

Nesbit²,

Harding³

et al. 2005

J. Clin. Invest.

135

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show abstract

“…Overlapping PACs 71-C21 and 286-D6 were identified by hybridisation to oligonucleotide dACAGAAGGCTCGCACTATCGT, derived from the T7 end of PAC 79-L8. Cosmid 176g8 from the LL01NC01 library (Gingrich et al 1996;Trask et al 1991) was identified by hybridisation to a 311-bp PCR product from the 5' end of DFFB, amplified from genomic DNA. The primers for this PCR were dCCCTTTGACATG-GACAGCTGC and dTGCTTCCGCTTCAACCTTGT.…”

Section: Methodsmentioning

confidence: 99%

Structure and mutation analysis of the gene encoding DNA fragmentation factor 40 (caspase-activated nuclease), a candidate neuroblastoma tumour suppressor gene

et al. 2000

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We have characterised the DFFB gene, encoding the active subunit of the apoptotic nuclease DNA fragmentation factor (DFF40). DFFB maps to 1p36, near the imprinted putative tumour suppressor gene TP73. The DFFA gene (encoding the inhibitory DFF45 subunit) also maps to 1p36.2-36.3, and we show by FISH that DFFB lies distal to DFFA. We have also mapped a processed DFFB pseudogene to chromosome 9. DFFB itself has seven coding exons spanning 10 kb. Exhaustive mutation screening of 41 neuroblastomas and other tumours in which a 1p36 tumour suppressor gene is implicated showed no tumour-specific mutations. A coding region polymorphism was used to demonstrate uniformly biallelic expression in human fetal DFFB transcripts. Since the putative neuroblastoma tumour suppressor gene in distal 1p36 is predicted to be maternally expressed, the lack of imprinting and absence of somatic mutations in DFFB indicate that it is probably not the neuroblastoma tumour suppressor gene.

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“…Approximately 25 ng single-copy 3q26 region marker probes were used to screen gridded yeast artificial chromosome (YAC) libraries ( Chumakov et al 1992 ;Anand et al 1990 ;Larin et al 1991 ), the RPCI-1 P1 artificial chromosome (PAC) library ( Ioannou et al 1994 ), the RPCI-11 BAC library ( Osoegawa et al 2001 ), and the Lawrence Livermore National Laboratory chromosome-3-specific cosmid library, constructed by using the method of Gingrich et al (1996) . Filters were hybridised in 0.5 M phosphate buffer with 7% SDS and 1% bovine serum albumin overnight at 65°C and washed in 2× SSC/0.1%SDS (1× SSC = 150 mM NaCl, 15 mM sodium citrate, pH 7.0) at room temperature before exposure to film.…”

Section: Contig Assembly As An Aid To Defining the 3q26 Translocationmentioning

confidence: 99%

A giant novel gene undergoing extensive alternative splicing is severed by a Cornelia de Lange-associated translocation breakpoint at 3q26.3

et al. 2004

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Cornelia de Lange syndrome (CdLS) is a rare developmental malformation syndrome characterised by mental handicap, growth retardation, distinctive facial features and limb reduction defects. The vast majority of CdLS cases are sporadic. We carried out a high density bacterial artificial chromosome (BAC) microarray comparative genome hybridisation screen but no evidence was found for a consistent pattern of microdeletion/micro-duplication. As an alternative, we focused on identifying chromosomal regions spanning associated translocation breakpoints. We prioritised the distal 3q region because of the occurrence, in a classical CdLS patient, of a de novo balanced translocation with a breakpoint at 3q26.3 and of reports of phenotypic overlap between cases of mild CdLS and individuals trisomic for the 3q26-q27 region. We show that the 3q26.3 breakpoint severs a previously uncharacterised giant gene, NAALADL2, containing at least 32 exons spanning 1.37 Mb. Northern blot analysis identified up to six different transcripts in the 1-10 kb range with strongest expression in kidney and placenta; embryonic expression was largely confined to duodenal and stomach endoderm, mesonephros, metanephros and pancreas. Transcript analysis identified extensive alternative splicing leading to multiple 5′ and 3′ untranslated regions and variable coding sequences. Multiple protein isoforms were defined by different N-terminal regions (with at least four alternative initiating methionine codons), and by differential protein truncation/use of alternative C-terminal sequences attributable to alternative splicing/polyadenylation. Outside the N-terminal regions, the predicted proteins showed significant homology to N-acetylated alpha-linked acidic dipeptidase and transferrin receptors. Mutation screening of NAALADL2 in a panel of CdLS patient DNA samples failed to identify patient-specific mutations. We discuss the possibility that the 3q26.3 translocation could nevertheless contribute to pathogenesis. Tonkin et al.

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Construction and Characterization of Human Chromosome 2-Specific Cosmid, Fosmid, and PAC Clone Libraries

Cited by 25 publications

References 0 publications

An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism

An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism

Structure and mutation analysis of the gene encoding DNA fragmentation factor 40 (caspase-activated nuclease), a candidate neuroblastoma tumour suppressor gene

A giant novel gene undergoing extensive alternative splicing is severed by a Cornelia de Lange-associated translocation breakpoint at 3q26.3

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