Instability of bacterial artificial chromosome (BAC) clones containing tandemly repeated DNA sequences

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 463-469 ◽  
Author(s):  
Junqi Song ◽  
Fenggao Dong ◽  
Jason W Lilly ◽  
Robert M Stupar ◽  
Jiming Jiang
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Early Stage ◽  
Repeated Dna ◽  
Genome Research ◽  
Bac Clone ◽  
Artificial Chromosomes ◽  
Bac Clones ◽  
The Impact ◽  
Tandemly Repeated Dna

The cloning and propagation of large DNA fragments as bacterial artificial chromosomes (BACs) has become a valuable technique in genome research. BAC clones are highly stable in the host, Escherichia coli, a major advantage over yeast artificial chromosomes (YACs) in which recombination-induced instability is a major drawback. Here we report that BAC clones containing tandemly repeated DNA elements are not stable and can undergo drastic deletions during routine library maintenance and DNA preparation. Instability was observed in three BAC clones from sorghum, rice, and potato, each containing distinct tandem repeats. As many as 46% and 74% of the single colonies derived from a rice BAC clone containing 5S ribosomal RNA genes had insert deletions after 24 and 120 h of growth, respectively. We also demonstrated that BAC insert rearrangement can occur in the early stage of library construction and duplication. Thus, a minimum growth approach may not avoid the instability problem of such clones. The impact of BAC instability on genome research is discussed.Key words: repetitive DNA, large insert DNA library, genome research.

scholarly journals Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome.

1984 ◽  
Vol 4 (2) ◽  
pp. 254-259 ◽  
Author(s):  
D Carroll ◽  
J E Garrett ◽  
B S Lam
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Genomic Organization ◽  
Evolutionary Conservation ◽  
Repeated Dna ◽  
Flanking Sequence ◽  
Base Pairs ◽  
Selection For ◽  
Tandemly Repeated Dna

There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each type is variable from cluster to cluster and averages about seven of each type per cluster. Every cluster has ca. 1,000 base pairs of common left flanking sequence (adjacent to the PTR-1 repeats) and 1,000 base pairs of common right flanking sequence (adjacent to the PTR-2 repeats). Beyond these common flanks, the DNA sequences are different in the eight cloned genomic fragments we have studied. Thus, the hundreds of PTR clusters in the genome are dispersed at apparently unrelated sites. Nucleotide sequences of representative PTR-1 and PTR-2 repeats are 64% homologous. These sequences do not reveal an obvious function. However, the related species X. mulleri and X. borealis have sequences homologous to PTR-1 and PTR-2, which show the same repeat lengths and genomic organization. This evolutionary conservation suggests positive selection for the clusters. Maintenance of these sequences at dispersed sites imposes constraints on possible mechanisms of concerted evolution.

Isolated clusters of paired tandemly repeated sequences in the Xenopus laevis genome

1984 ◽  
Vol 4 (2) ◽  
pp. 254-259
Author(s):  
D Carroll ◽  
J E Garrett ◽  
B S Lam
Keyword(s):  
Xenopus Laevis ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Genomic Organization ◽  
Evolutionary Conservation ◽  
Repeated Dna ◽  
Flanking Sequence ◽  
Base Pairs ◽  
Selection For ◽  
Tandemly Repeated Dna

There exist in the Xenopus laevis genome clusters of tandemly repeated DNA sequences, consisting of two types of 393-base-pair repeating unit. Each such cluster contains several units of one of these paired tandem repeats (PTR-1), followed by several units of the other repeat (PTR-2). The number of repeats of each type is variable from cluster to cluster and averages about seven of each type per cluster. Every cluster has ca. 1,000 base pairs of common left flanking sequence (adjacent to the PTR-1 repeats) and 1,000 base pairs of common right flanking sequence (adjacent to the PTR-2 repeats). Beyond these common flanks, the DNA sequences are different in the eight cloned genomic fragments we have studied. Thus, the hundreds of PTR clusters in the genome are dispersed at apparently unrelated sites. Nucleotide sequences of representative PTR-1 and PTR-2 repeats are 64% homologous. These sequences do not reveal an obvious function. However, the related species X. mulleri and X. borealis have sequences homologous to PTR-1 and PTR-2, which show the same repeat lengths and genomic organization. This evolutionary conservation suggests positive selection for the clusters. Maintenance of these sequences at dispersed sites imposes constraints on possible mechanisms of concerted evolution.

The molecular structure, chromosomal organization, and interspecies distribution of a family of tandemly repeated DNA sequences of Antirrhinum majus L.

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 243-248 ◽  
Author(s):  
Thomas Schmidt ◽  
Jörg Kudla
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Antirrhinum Majus ◽  
Repeated Dna ◽  
Satellite Dnas ◽  
Repeated Dna Sequences ◽  
The North ◽  
Tandemly Repeated Dna

Monomers of a major family of tandemly repeated DNA sequences of Antirrhinum majus have been cloned and characterized. The repeats are 163–167 bp long, contain on average 60% A + T residues, and are organized in head-to-tail orientation. According to site-specific methylation differences two subsets of repeating units can be distinguished. Fluorescent in situ hybridization revealed that the repeats are localized at centromeric regions of six of the eight chromosome pairs of A. majus with substantial differences in array size. The monomeric unit shows no homologies to other plant satellite DNAs. The repeat exists in a similar copy number and conserved size in the genomes of six European species of the genus Antirrhinum. Tandemly repeated DNA sequences with homology to the cloned monomer were also found in the North American section Saerorhinum, indicating that this satellite DNA might be of ancient origin and was probably already present in the ancestral genome of both sections. Key words : Antirrhinum majus, satellite DNA, repetitive DNA, methylation, in situ hybridization.

Breakage of the human Y-chromosome short arm between two blocks of tandemly repeated DNA sequences

Genomics ◽  
1989 ◽  
Vol 5 (1) ◽  
pp. 153-156 ◽  
Author(s):  
Ulrich Müller ◽  
Marc Lalande ◽  
Timothy A. Donlon ◽  
Michael W. Heartlein
Keyword(s):  
Y Chromosome ◽  
Dna Sequences ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Human Y Chromosome ◽  
Tandemly Repeated Dna

FokI DNA repeats in the genome of Vicia faba: species specificity, structure, redundancy modulation, and nuclear organization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1255-1261 ◽  
Author(s):  
F. Maggini ◽  
R. D'Ovidio ◽  
M. T. Gelati ◽  
M. Frediani ◽  
R. Cremonini ◽  
...  
Keyword(s):  
Vicia Faba ◽  
Dna Sequences ◽  
Nuclear Organization ◽  
Chromosome Complement ◽  
Dna Repeats ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Functional Roles ◽  
Species Specific ◽  
Tandemly Repeated Dna

Tandemly repeated DNA sequences about 60 bp in length, which may be isolated by digestion with FokI restriction endonuclease, were studied by means of molecular and cytological hybridizations in Vicia faba and other Vicia species. The results obtained can be summarized as follows: (i) FokI repeats are almost species specific to V. faba, since they hybridize to a minimum extent to the genomic DNA of only two out of five related species; (ii) these tandemly repeated elements display variability in structure even within one and the same array, where different repeats may share not more than 71% homology; (iii) their redundancy in the genome of V. faba is remarkably high and varies largely between land races (copy numbers per haploid, 1C, genome range from 21.51 × 106 to 5.39 × 106); (iv) FokI repeats are clustered in differing amounts in each subtelocentric pair of the chromosome complement and are missing or present in a nondetectable amount in the submetacentric pair; (vi) chromosome regions that bear these repeats associate closely to varying degrees in interphase nuclei. These results are discussed in relation to possible functional roles that tandemly repeated DNA sequences such as the FokI elements might play.Key words: FokI, intraspecific DNA changes, nuclear organization, repeated DNA sequences, Vicia faba.

scholarly journals Tandemly repeated DNA sequences in Brassicaceae: A characterization of the sequences in Cochlearia officinalis and Isatis tinctoria

Hereditas ◽  
2008 ◽  
Vol 113 (3) ◽  
pp. 291-295 ◽  
Author(s):  
CHRISTER HALLDéN ◽  
MIKAEL SVENSSON ◽  
TOMAS BRYNGELSSON ◽  
CHRISTINA LIND
Keyword(s):  
Dna Sequences ◽  
Repeated Dna ◽  
Isatis Tinctoria ◽  
Repeated Dna Sequences ◽  
Tandemly Repeated Dna
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