THE MOLECULAR THROUGH ECOLOGICAL GENETICS OF ABNORMAL ABDOMEN. II. RIBOSOMAL DNA POLYMORPHISM IS ASSOCIATED WITH THE ABNORMAL ABDOMEN SYNDROME IN DROSOPHILA MERCATORUM

ABSTRACT Restriction endonuclease cleavage analyses of cloned and genomic DNA samples indicate that the structure of the DNA encoding the large cytoplasmic RNAs (rDNAs) is altered in Drosophila mercatorum lines which exhibit an abnormal abdomen (aa) phenotype. In a majority of the rDNA repeat units from aa flies, the 28S coding sequence is interrupted by a large [5-6 kilobase pairs (kbp)] insert. A subclone containing this inserted DNA (ins 3) hybridizes primarily to rDNA-containing sequences in in situ and genomic blot hybridization experiments. Additionally, genomic nitrocellulose blot hybridization analyses show that ins - containing rDNA repeat units are clustered in a spontaneously arising aa mutant. This rDNA alteration in D. mercatorum flies with the aa phenotype more closely resembles the bobbed (bb) defect of D. hydei than the bb defect of D. melanogaster, which involves alterations in rDNA copy number. By analogy with the other Drosophila systems, we propose that the altered D. mercatorum rDNA repeat units are defective in rRNA production at a critical stage. The lowered levels of rRNA ultimately would limit the concentration of ribosomes needed to produce large quantities of a protein (in these cases, juvenile hormone esterase) needed for normal development.

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5S ribosomal RNA genes in six species of Mediterranean grey mullets: genomic organization and phylogenetic inference

Genome ◽

10.1139/g07-058 ◽

2007 ◽

Vol 50 (9) ◽

pp. 787-795 ◽

Cited By ~ 27

Author(s):

Ekaterina Gornung ◽

Paolo Colangelo ◽

Flavia Annesi

Keyword(s):

Ribosomal Rna ◽

Blot Hybridization ◽

5S Rdna ◽

Ribosomal Rna Genes ◽

Rdna Repeat ◽

Data Set ◽

Single Chromosome ◽

5S Ribosomal Rna ◽

Repeat Units ◽

Rna Genes

This paper describes a study of the 5S ribosomal RNA genes (5S rDNA) in a group of 6 species belonging to 4 genera of Mugilidae. In these 6 species, the relatively short 5S rDNA repeat units, generated by PCR and ranging in size from 219 to 257 bp, show a high level of intragenomic homogeneity of both coding and spacer regions (NTS-I). Phylogenetic reconstructions based on this data set highlight the greater phylogenetic and genetic diversity of Mugil cephalus and Oedalechilus labeo compared with the genera Liza and Chelon. Comparative sequence analysis revealed significant conservation of the short 5S rDNA repeat units across Chelon and Liza. Moreover, a second size class of 5S rDNA repeat units, ranging from roughly 800 to 1100 bp, was produced in the Liza and Chelon samples. Only short 5S rDNA repeat units were found in M. cephalus and O. labeo. The sequences of the long 5S rDNA repeat units, obtained in Chelon labrosus and Liza ramada , differ owing to the presence of 2 large insertion/deletions (indels) in the spacers (NTS-II) and show considerable sequence identity with NTS-I spacers. Interspecific sequence variation of NTS-II spacers, excluding the indels, is low. Southern-blot hybridization patterns suggest an intermixed arrangement of short and long repeat units within a single chromosome locus.

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The Ecological Genetics of Abnormal Abdomen in Drosophila mercatorum

Ecological and Evolutionary Genetics of Drosophila ◽

10.1007/978-1-4684-8768-8_3 ◽

1990 ◽

pp. 17-35 ◽

Cited By ~ 8

Author(s):

Alan R. Templeton ◽

Hope Hollocher ◽

Susan Lawler ◽

J. Spencer Johnston

Keyword(s):

Ecological Genetics ◽

Drosophila Mercatorum

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Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae – Saccharinae)

Genome ◽

10.1139/g97-057 ◽

1997 ◽

Vol 40 (4) ◽

pp. 428-432 ◽

Cited By ~ 17

Author(s):

P. Besse ◽

C. L. McIntyre ◽

D. M. Burner ◽

C. G. de Almeida

Keyword(s):

Genomic Dna ◽

Blot Hybridization ◽

Female Parent ◽

Saccharum Officinarum ◽

Rapid Screening ◽

Hybridization Technique ◽

Slot Blot ◽

Saccharum Species ◽

Slot Blot Hybridization

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum × Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum × Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.Key words: slot blot, Erianthus, genomic DNA, Saccharum, sugarcane.

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cDNA cloning, expression and chromosomal localization of the human sarco/endoplasmic reticulum Ca2+-ATPase 3 gene

Biochemical Journal ◽

10.1042/bj3180689 ◽

1996 ◽

Vol 318 (2) ◽

pp. 689-699 ◽

Cited By ~ 35

Author(s):

Leonard DODE ◽

Frank WUYTACK ◽

Patrick F. J. KOOLS ◽

Fouzia BABA-AISSA ◽

Luc RAEYMAEKERS ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Nucleotide Sequence ◽

Blot Hybridization ◽

Cdna Probe ◽

Human Platelets ◽

Gene Transcript ◽

Northern Blot Hybridization ◽

Dna Encoding ◽

Coding Region ◽

Cos Cells

cDNA and genomic clones encoding human sarco/endoplasmic reticulum Ca2+-ATPase 3 (SERCA3) were isolated. The composite nucleotide sequence of the 4.6 kb cDNA, as well as the partial structure of 25 kb of genomic DNA encoding all but the 5´ region of the gene, was determined. The nucleotide sequence coding for the last six amino acids of the pump and the 3´-untranslated region were identified within the sequence of the last exon. Northern blot hybridization analysis using cDNA probes derived from this exon detected a 4.8 kb transcript in several human tissues. Using a cDNA probe derived from the 5´-coding region an unexpected mRNA distribution pattern, consisting of two mRNA species of 4.8 and 4.0 kb, was detected in thyroid gland and bone marrow only. This is the first indication of an alternative splicing mechanism operating on the SERCA3 gene transcript, which most likely generates SERCA3 isoforms with altered C-termini. Human SERCA3 expressed in platelets and in COS cells transfected with the corresponding cDNA was detected with the previously described antibody N89 (directed against the N-terminal region of rat SERCA3) and with a new SERCA3-specific antiserum C91, directed against the extreme C-terminus of the human isoform. A monoclonal antibody PL/IM430, previously assumed to recognize SERCA3 in human platelets, does not react with the 97 kDa human SERCA3 transiently expressed in COS cells. Therefore the 97 kDa isoform detected by PL/IM430 more likely represents a novel SERCA pump, as recently suggested [Kovács, Corvazier, Papp, Magnier, Bredoux, Enyedi, Sarkadi and Enouf (1994) J. Biol. Chem. 269, 6177–6184]. Finally, by fluorescence in situ hybridization and chromosome G-banding analyses, the SERCA3 gene was assigned to human chromosome 17p13.3.

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The molecular through ecological genetics of abnormal abdomen. IV. Components of genetic variation in a natural population of Drosophila mercatorum.

Genetics ◽

10.1093/genetics/130.2.355 ◽

1992 ◽

Vol 130 (2) ◽

pp. 355-366

Author(s):

H Hollocher ◽

A R Templeton ◽

R DeSalle ◽

J S Johnston

Keyword(s):

Genetic Variation ◽

Natural Population ◽

Allelic Variation ◽

Natural Populations ◽

Developmental Time ◽

Ecological Genetics ◽

Adult Longevity ◽

Genetic Determinants ◽

Drosophila Mercatorum ◽

Y Chromosomes

Abstract Natural populations of Drosophila mercatorum are polymorphic for a phenotypic syndrome known as abnormal abdomen (aa). This syndrome is characterized by a slow-down in egg-to-adult developmental time, retention of juvenile abdominal cuticle in the adult, increased early female fecundity, and decreased adult longevity. Previous studies revealed that the expression of this syndrome in females is controlled by two closely linked X chromosomal elements: the occurrence of an R1 insert in a third or more of the X-linked 28S ribosomal genes (rDNA), and the failure of replicative selection favoring uninserted 28S genes in larval polytene tissues. The expression of this syndrome in males in a laboratory stock was associated with the deletion of the rDNA normally found on the Y chromosome. In this paper we quantify the levels of genetic variation for these three components in a natural population of Drosophila mercatorum found near Kamuela, Hawaii. Extensive variation is found in the natural population for both of the X-linked components. Moreover, there is a significant association between variation in the proportion of R1 inserted 28S genes with allelic variation at the underreplication (ur) locus such that both of the necessary components for aa expression in females tend to cosegregate in the natural population. Accordingly, these two closely linked X chromosomal elements are behaving as a supergene in the natural population. Because of this association, we do not believe the R1 insert to be actively transposing to an appreciable extent. The Y chromosomes extracted from nature are also polymorphic, with 16% of the Ys lacking the Y-specific rDNA marker. The absence of this marker is significantly associated with the expression of aa in males. Hence, all three of the major genetic determinants of the abnormal abdomen syndrome are polymorphic in this natural population.

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Age-dependent ribosomal DNA variations and their effect on cellular function in mammalian cells

10.1101/2020.07.10.196840 ◽

2020 ◽

Author(s):

Eriko Watada ◽

Sihan Li ◽

Yutaro Hori ◽

Katsunori Fujiki ◽

Katsuhiko Shirahige ◽

...

Keyword(s):

Ribosomal Rna ◽

Copy Number ◽

Mammalian Cells ◽

Bone Marrow Cells ◽

Budding Yeast ◽

Rdna Repeat ◽

Age Dependent ◽

Old Mice ◽

Rdna Copy ◽

Rdna Copy Number

AbstractThe ribosomal RNA gene, which consists of tandem repetitive arrays (rDNA repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in ageing mammalian cells. Using quantitative analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. Moreover, the level of pre-rRNA transcripts was reduced in older BALB/cA mice. We also identified many sequence variations among the repeats with two mutations being unique to old mice. These sequences were conserved in budding yeast and equivalent mutations shortened the yeast chronological lifespan. Our findings suggest that rDNA is also fragile in mammalian cells and alterations within this region have a profound effect on cellular function.Author SummaryThe ribosomal RNA gene (rDNA) is one of the most unstable regions in the genome due to its tandem repetitive structure. rDNA copy number in the budding yeast increases and becomes unstable as the cell ages. It is speculated that the rDNA produces an “aging signal” inducing senescence and death. However, it is unclear how the rDNA repeat changes during the aging process in mammalian cells. In this study, we attempted to identify the age-dependent alteration of rDNA in mice. Using quantitative single cell analysis, we show that rDNA copy number increases in old mice bone marrow cells. By contrast, the level of ribosomal RNA production was reduced because of increased levels of DNA methylation that represses transcription. We also identified many sequence variations in the rDNA. Among them, three mutations were unique to old mice and two of them were found in the conserved region in budding yeast. We then established a yeast strain with the old mouse-specific mutations and found this shortened the lifespan of the cells. These findings suggest that rDNA is also fragile in mammalian cells and alteration to this region of the genome affects cellular senescence.

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The molecular through ecological genetics of abnormal abdomen in Drosophila mercatorum. VI. The non-neutrality of the Y chromosome rDNA polymorphism.

Genetics ◽

10.1093/genetics/136.4.1373 ◽

1994 ◽

Vol 136 (4) ◽

pp. 1373-1384

Author(s):

H Hollocher ◽

A R Templeton

Keyword(s):

Y Chromosome ◽

Adult Development ◽

Sexual Maturation ◽

Development Time ◽

Ecological Genetics ◽

Pleiotropic Effects ◽

Naturally Occurring ◽

Drosophila Mercatorum ◽

Rdna Polymorphism ◽

Male Expression

Abstract An association between quantitative variation of rDNA on the Y chromosome and male expression of the juvenilized, adult cuticle of the abnormal abdomen syndrome has been found for Drosophila mercatorum. Many pleiotropic effects of this syndrome have been described previously for females, but little was known about possible pleiotropic effects in males. The effects on males open up new avenues for the action of natural selection operating on the system. In females, the syndrome causes an increase in egg-to-adult development time, precocious sexual maturation, increased fecundity and decreased longevity. In addition to the cuticle phenotype, in males abnormal abdomen causes delayed sexual maturation, increased longevity, and decreased mating success, yet no change in egg-to-adult development time. Thus the syndrome has opposing fitness effects in the two sexes, which may help explain the genetic polymorphism observed in this system. Although investigated intensively, associations between naturally occurring Y-linked polymorphism and fitness phenotypes have not been found in Drosophila melanogaster.

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Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽

10.3390/insects10090306 ◽

2019 ◽

Vol 10 (9) ◽

pp. 306 ◽

Cited By ~ 1

Author(s):

Pablo Mora ◽

Jesús Vela ◽

Areli Ruiz-Mena ◽

Teresa Palomeque ◽

Pedro Lorite

Keyword(s):

Repetitive Dna ◽

Satellite Dna ◽

Repeat Unit ◽

Pericentromeric Region ◽

Fish Analysis ◽

Agricultural Pests ◽

Base Pairs ◽

Satellite Dnas ◽

Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

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Molecular characterization and expression of the stratification-related cytokeratins 4 and 15.

The Journal of Cell Biology ◽

10.1083/jcb.106.4.1249 ◽

1988 ◽

Vol 106 (4) ◽

pp. 1249-1261 ◽

Cited By ~ 98

Author(s):

R E Leube ◽

B L Bader ◽

F X Bosch ◽

R Zimbelmann ◽

T Achtstaetter ◽

...

Keyword(s):

Basal Cell ◽

Blot Hybridization ◽

Northern Blot Hybridization ◽

Type I ◽

Specific Expression ◽

Genes Encoding ◽

Cell Layers ◽

Hybridization In Situ ◽

Stratified Epithelia

A number of human cytokeratins are expressed during the development of stratified epithelia from one-layered polar epithelia and continue to be expressed in several adult epithelial tissues. For studies of the regulation of the synthesis of stratification-related cytokeratins in internal tissues, we have prepared cDNA and genomic clones encoding cytokeratin 4, as a representative of the basic (type II) cytokeratin subfamily and cytokeratin 15, as representative of the acidic (type I) subfamily, and determined their nucleotide sequences. The specific expression of mRNAs encoding these two polypeptides in certain stratified tissues and cultured cell lines is demonstrated by Northern blot hybridization. Hybridization in situ with antisense riboprobes and/or synthetic oligonucleotides shows the presence of cytokeratin 15 mRNA in all layers of esophagus, whereas cytokeratin 4 mRNA tends to be suprabasally enriched, although to degrees varying in different regions. We conclude that the expression of the genes encoding these stratification-related cytokeratins starts already in the basal cell layer and does not depend on vertical differentiation and detachment from the basal lamina. Our results also show that simple epithelial and stratification-related cytokeratins can be coexpressed in basal cell layers of certain stratified epithelia such as esophagus. Implications of these findings for epithelial differentiation and the formation of squamous cell carcinomas are discussed.

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