Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 657-665 ◽  
Author(s):  
Guy Drouin
Keyword(s):  
Dna Sequences ◽  
Germ Line ◽  
Somatic Cells ◽  
Repeated Sequences ◽  
Cyclopoid Copepod ◽  
Embryonic Cells ◽  
Repeated Dna ◽  
Chromatin Diminution ◽  
Mesocyclops Edax ◽  
Tandemly Repeated Dna

Chromatin diminution, i.e., the loss of selected chromosomal regions during the differentiation of early embryonic cells into somatic cells, has been described in taxa as varied as ciliates, copepods, insects, nematodes, and hagfish. The nature of the eliminated DNA has been extensively studied in ciliate, nematode, and hagfish species. However, the small size of copepods, which makes it difficult to obtain enough DNA from early embryonic cells for cloning and sequencing, has limited such studies. Here, to identify the sequences eliminated from the somatic cells of a copepod species that undergoes chromatin diminution, we randomly amplified DNA fragments from germ line and somatic line cells of Mesocyclops edax, a freshwater cyclopoid copepod. Of 47 randomly amplified germ line clones, 45 (96%) contained short, tandemly repeated sequences composed of either 2 bp CA-repeats, 8 bp CAAATAGA-repeats, or 9 bp CAAATTAAA-repeats. In contrast, of 83 randomly amplified somatic line clones, only 47 (57%) contained such short, tandemly repeated sequences. As previously observed in some nematode species, our results therefore show that there is partial elimination of chromosomal regions containing (CAAATAGA and CAAATTAAA) repeated sequences during the chromatin diminution observed in the somatic cells of M. edax. We speculate that chromatin diminution might have evolved repeatedly by recruitment of RNAi-related mechanisms to eliminate nonfunctional tandemly repeated DNA sequences from the somatic genome of some species.Key words: chromatin diminution, Mesocyclops edax, copepod, satellite DNA, hetorochromatin.

Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 944-953 ◽  
Author(s):  
Xinping Zhao ◽  
Gary Kochert
Keyword(s):  
Dna Sequences ◽  
Blot Hybridization ◽  
Rice Genome ◽  
Repeated Sequence ◽  
Repeated Sequences ◽  
Repeated Dna ◽  
Rice Varieties ◽  
Slot Blot Hybridization ◽  
Repeated Dna Sequence ◽  
Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

Insertion and excision of Caenorhabditis elegans transposable element Tc1

1988 ◽  
Vol 8 (2) ◽  
pp. 737-746
Author(s):  
D Eide ◽  
P Anderson
Keyword(s):  
Amino Acid ◽  
Caenorhabditis Elegans ◽  
Transposable Element ◽  
Dna Sequences ◽  
Germ Line ◽  
Consensus Sequence ◽  
Somatic Cells ◽  
Chain Gene ◽  
Imprecise Excision ◽  
Insertion Sites

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

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

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 Functional analysis of a centromere from fission yeast: a role for centromere-specific repeated DNA sequences.

1990 ◽  
Vol 10 (5) ◽  
pp. 1863-1872 ◽  
Author(s):  
L Clarke ◽  
M P Baum
Keyword(s):  
Dna Sequences ◽  
Inverted Repeat ◽  
Repeated Sequence ◽  
Repeated Sequences ◽  
Central Core ◽  
Repeated Dna ◽  
Inverted Repeat Region ◽  
Repeated Dna Sequences ◽  
Centromere Function ◽  
Chromosome Ii

A circular minichromosome carrying functional centromere sequences (cen2) from Schizosaccharomyces pombe chromosome II behaves as a stable, independent genetic linkage group in S. pombe. The cen2 region was found to be organized into four large tandemly repeated sequence units which span over 80 kilobase pairs (kb) of untranscribed DNA. Two of these units occurred in a 31-kb inverted repeat that flanked a 7-kb central core of nonhomology. The inverted repeat region had centromere function, but neither the central core alone nor one arm of the inverted repeat was functional. Deletion of a portion of the repeated sequences that flank the central core had no effect on mitotic segregation functions or on meiotic segregation of a minichromosome to two of the four haploid progeny, but drastically impaired centromere-mediated maintenance of sister chromatid attachment in meiosis I. This requirement for centromere-specific repeated sequences could not be satisfied by introduction of random DNA sequences. These observations suggest a function for the heterochromatic repeated DNA sequences found in the centromere regions of higher eucaryotes.

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