Nonrandom distribution of long mono- and dinucleotide repeats in Drosophila chromosomes: correlations with dosage compensation, heterochromatin, and recombination

1989 ◽  
Vol 9 (3) ◽  
pp. 1173-1182
Author(s):  
K Lowenhaupt ◽  
A Rich ◽  
M L Pardue
Keyword(s):  
Y Chromosome ◽  
Dna Sequences ◽  
Polytene Chromosomes ◽  
Drosophila Species ◽  
Repeated Dna ◽  
Dinucleotide Repeats ◽  
Order Of Magnitude ◽  
The Individual ◽  
And Function

Long stretches of (dC-dA)n.(dT-dG)n, abbreviated CA/TG, have a distinctive distribution on Drosophila chromosomes (M.L. Pardue, K. Lowenhaupt, A. Rich, and A. Nordheim, EMBO J. 6:1781-1789, 1987). The distribution of CA/TG suggests a correlation with the overall transcriptional activity of chromosomal regions and with the ability to undergo meiotic recombination. These correlations are conserved among Drosophila species and may indicate one or more chromosomal functions. To test the generality of these findings, we analyzed the distribution of the rest of the six possible mono- and dinucleotide repeats (A/T, C/G, AT/AT, CA/TG, CT/AG, and CG/CG). All but CG/CG were present at significant levels in the genomes of the six Drosophila species studied; however, A/T levels were an order of magnitude lower than those of the other sequences. Data base analyses suggested that the same sequences are present in other eucaryotes. Like CA/TG, both CT/AG and C/G showed increased levels on dosage-compensating chromosomes; however, the individual sites clearly differed for each sequence. In contrast, A/T and AT/AT, although present in Drosophila DNA, could not be detected in situ in polytene chromosomes. We also used in situ hybridization to analyze the neo-Y chromosome of Drosophila miranda, an ancestral autosome that has become attached to the Y chromosome and is now partially heterochromatic. The neo-Y has acquired repeated DNA sequences; we found that the added sequences are as devoid of mono- and dinucleotide repeats as other heterochromatin. The distribution and function of these sequences are likely to result from both their repetitious nature and base contents.

scholarly journals Nonrandom distribution of long mono- and dinucleotide repeats in Drosophila chromosomes: correlations with dosage compensation, heterochromatin, and recombination.

1989 ◽  
Vol 9 (3) ◽  
pp. 1173-1182 ◽  
Author(s):  
K Lowenhaupt ◽  
A Rich ◽  
M L Pardue
Keyword(s):  
Y Chromosome ◽  
Dna Sequences ◽  
Polytene Chromosomes ◽  
Drosophila Species ◽  
Repeated Dna ◽  
Dinucleotide Repeats ◽  
Order Of Magnitude ◽  
The Individual ◽  
And Function

Long stretches of (dC-dA)n.(dT-dG)n, abbreviated CA/TG, have a distinctive distribution on Drosophila chromosomes (M.L. Pardue, K. Lowenhaupt, A. Rich, and A. Nordheim, EMBO J. 6:1781-1789, 1987). The distribution of CA/TG suggests a correlation with the overall transcriptional activity of chromosomal regions and with the ability to undergo meiotic recombination. These correlations are conserved among Drosophila species and may indicate one or more chromosomal functions. To test the generality of these findings, we analyzed the distribution of the rest of the six possible mono- and dinucleotide repeats (A/T, C/G, AT/AT, CA/TG, CT/AG, and CG/CG). All but CG/CG were present at significant levels in the genomes of the six Drosophila species studied; however, A/T levels were an order of magnitude lower than those of the other sequences. Data base analyses suggested that the same sequences are present in other eucaryotes. Like CA/TG, both CT/AG and C/G showed increased levels on dosage-compensating chromosomes; however, the individual sites clearly differed for each sequence. In contrast, A/T and AT/AT, although present in Drosophila DNA, could not be detected in situ in polytene chromosomes. We also used in situ hybridization to analyze the neo-Y chromosome of Drosophila miranda, an ancestral autosome that has become attached to the Y chromosome and is now partially heterochromatic. The neo-Y has acquired repeated DNA sequences; we found that the added sequences are as devoid of mono- and dinucleotide repeats as other heterochromatin. The distribution and function of these sequences are likely to result from both their repetitious nature and base contents.

Molecular Cytogenetic Analysis of Karyotype and Y Chromosome Conservation in Species of the Genus Talpa (Insectivora)

2020 ◽  
Vol 160 (5) ◽  
pp. 264-271
Author(s):  
Juana Gutierrez ◽  
Gael Aleix-Mata ◽  
Juan A. Marchal ◽  
María Arroyo ◽  
Riccardo Castiglia ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Y Chromosome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Chromosome Painting ◽  
Chromosomal Mapping ◽  
Repeated Dna ◽  
Molecular Cytogenetic ◽  
Y Chromosomes ◽  
Cytogenetic Analyses

The Talpidae family has a highly stable karyotype. Most of the chromosome studies in this mammal group, however, employed classical cytogenetic techniques. Molecular cytogenetic analyses are still scarce and, for example, no repeated DNA sequences have been described to date. In this work, we used sequence analysis, chromosomal mapping of a LINE1 retroelement sequence, as well as chromosome painting with a whole Y chromosome probe of T. occidentalis to compare the karyotypes of 3 species of the genus Talpa (T. occidentalis, T. romana, and T. aquitania). Our results demonstrate that in Talpa genomes LINE1 sequences are widely distributed on all chromosomes but are enriched in pericentromeric C-band-positive regions. In addition, these LINE1 accumulate on the Y chromosomes of the 3 Talpa species regardless of their euchromatic or heterochromatic condition. Chromosome painting shows that the Y chromosomes in these 3 species are highly conserved. Interestingly, they share sequences with heterochromatic blocks on chromosome pairs 14 and 16 and, to a lesser degree, with the pericentromeric regions of other autosomes. Together, our analyses demonstrate that the repetitive DNA content of chromosomes from Talpa species is highly conserved.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1061-1069 ◽  
Author(s):  
A. Cuadrado ◽  
N. Jouve ◽  
C. Ceoloni
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Individual Identification ◽  
Highly Repetitive Dna ◽  
The Individual

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

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

Topographical mapping of ribosomal RNAs in situ by electron spectroscopic imaging

1984 ◽  
Vol 42 ◽  
pp. 690-691
Author(s):  
M. Boublik ◽  
G.T. Oostergetel ◽  
B. Frankland ◽  
F.P. Ottensmeyer
Keyword(s):  
Spectroscopic Techniques ◽  
Rna Molecules ◽  
Macromolecular System ◽  
Unique Distribution ◽  
Topographical Mapping ◽  
The Individual ◽  
And Function ◽  
Electron Energy Loss

Visualization of the in situ location of the individual components of any macromolecular system is important for understanding its assembly, interactions, and function. Ribosomes, which are small cellular organelles involved in protein synthesis are high molecular weight nucleoprotein complexes composed only of proteins and RNAs. This “simple” composition of ribosomes enables us topographical studies directed either towards localization of the individual ribosomal protein and RNA molecules or merely to the determination of the distribution of the protein and RNA moieties within the ribosome and its subunits. We have utilized the recent progress in the development of microanalytical electron spectroscopic techniques, electron energy loss spectroscopy (EELS) in particular, and the unique distribution of the phosphorus atoms on the ribosome (the phosphorus atoms are present only in the structural backbone of the rRNA) for the direct tracing of the RNA molecules in situ.

Redundant and cryptic enhancer activities of the Drosophila yellow gene

2018 ◽  
Author(s):  
Gizem Kalay ◽  
Jennifer Lachowiec ◽  
Ulises Rosas ◽  
Mackenzie R. Dome ◽  
Patricia Wittkopp
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Model System ◽  
Drosophila Species ◽  
Drosophila Pseudoobscura ◽  
Regulatory Sequences ◽  
Phenotypic Evolution ◽  
Evolutionary Changes ◽  
And Function

Abstractcis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale by comparing the distribution and function of yellow enhancer activities throughout the 5’ intergenic and intronic sequences of Drosophila melanogaster, Drosophila pseudoobscura, and Drosophila willistoni. We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of pre-existing cis-regulatory sequences.

RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L.

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 931-936 ◽  
Author(s):  
Koichi Sakamoto ◽  
Tomoko Abe ◽  
Tomoki Matsuyama ◽  
Shigeo Yoshida ◽  
Nobuko Ohmido ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Y Chromosome ◽  
Dna Sequences ◽  
Blot Analysis ◽  
Cannabis Sativa ◽  
Random Amplified Polymorphic Dna ◽  
Male And Female ◽  
Retrotransposable Elements

Male-associated DNA sequences were analyzed in Cannabis sativa L. (hemp), a dioecious plant with heteromorphic sex chromosomes. DNA was isolated from male and female plants and subjected to random amplified polymorphic DNA analysis. Of 120 primers, 17 yielded 400 to 1500-bp fragments detectable in male, but not female, plants. These fragments were cloned and used as probes in gel-blot analysis of genomic DNA. When male and female DNA was hybridized with 2 of these male-specific fragments, MADC(male-associated DNA sequences in C. sativa)3 and MADC4, particularly intense bands specific to male plants were detected in addition to bands common to both sexes. The MADC3 and MADC4 sequences were shown to encode gag/pol polyproteins of copia-like retrotransposons. Fluorescence in situ hybridization with MADC3 and MADC4 as probes revealed a number of intense signals on the Y chromosome as well as dispersed signals on all chromosomes. The gel-blot analysis and fluorescence in situ hybridization results presented here support the hypothesis that accumulation of retrotransposable elements on the Y chromosome might be 1 cause of heteromorphism of sex chromosomes.Key words: Cannabis sativa, FISH, RAPD, retrotransposon, sex chromosome.

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