scholarly journals Evidence that intergenic spacer repeats of Drosophila melanogaster rRNA genes function as X-Y pairing sites in male meiosis, and a general model for achiasmatic pairing.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 529-544 ◽  
Author(s):  
B D McKee ◽  
L Habera ◽  
J A Vrana
Keyword(s):  
Drosophila Melanogaster ◽  
Topoisomerase I ◽  
Meiotic Chromosome ◽  
Intergenic Spacer ◽  
Transcription Unit ◽  
P Element ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Meiotic Pairing ◽  
Rrna Transcription

Abstract In Drosophila melanogaster males, X-Y meiotic chromosome pairing is mediated by the nucleolus organizers (NOs) which are located in the X heterochromatin (Xh) and near the Y centromere. Deficiencies for Xh disrupt X-Y meiotic pairing and cause high frequencies of X-Y nondisjunction. Insertion of cloned rRNA genes on an Xh- chromosome partially restores normal X-Y pairing and disjunction. To map the sequences within an inserted, X-linked rRNA gene responsible for stimulating X-Y pairing, partial deletions were generated by P element-mediated destabilization of the insert. Complete deletions of the rRNA transcription unit did not interfere with the ability to stimulate X-Y pairing as long as most of the intergenic spacer (IGS) remained. Within groups of deletions that lacked the entire transcription unit and differed only in length of residual IGS material, pairing ability was proportional to the dose of 240-bp intergenic spacer repeats. Deletions of the complete rRNA transcription unit or the 28S sequences alone blocked nucleolus formation, as determined by binding of an antinucleolar antibody, yet did not interfere with pairing ability, suggesting that X-Y pairing may not be mechanistically related to nucleolus formation. A model for achiasmatic pairing in Drosophila males based upon the combined action of topoisomerase I and a strand transferase is proposed.

scholarly journals Patterns of Variation in the Intergenic Spacers of Ribosomal DNA in Drosophila melanogaster Support a Model for Genetic Exchanges During X-Y Pairing

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1221-1229
Author(s):  
Carlos Polanco ◽  
Ana I González ◽  
Gabriel A Dover
Keyword(s):  
Drosophila Melanogaster ◽  
Topoisomerase I ◽  
Natural Populations ◽  
Intergenic Spacer ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Chromosomal Distribution ◽  
Rdna Unit ◽  
Y Chromosomes ◽  
Its Regions

Abstract Detailed analysis of variation in intergenic spacer (IGS) and internal transcribed spacer (ITS) regions of rDNA drawn from natural populations of Drosophila melanogaster has revealed contrasting patterns of homogenization although both spacers are located in the same rDNA unit. On the basis of the role of IGS regions in X-Y chromosome pairing, we proposed a mechanism of single-strand exchanges at the IGS regions, which can explain the different evolutionary trajectories followed by the IGS and the ITS regions. Here, we provide data from the chromosomal distribution of selected IGS length variants, as well as the detailed internal structure of a large number of IGS regions obtained from specific X and Y chromosomes. The variability found in the different internal subrepeat regions of IGS regions isolated from X and Y chromosomes supports the proposed mechanism of genetic exchanges and suggests that only the “240” subrepeats are involved. The presence of a putative site for topoisomerase I at the 5′ end of the 18S rRNA gene would allow for the exchange between X and Y chromosomes of some 240 subrepeats, the promoter, and the ETS region, leaving the rest of the rDNA unit to evolve along separate chromosomal lineages. The phenomenon of localized units (modules) of homogenization has implications for multigene family evolution in general.

Multigene Family of Ribosomal DNA in Drosophila melanogaster Reveals Contrasting Patterns of Homogenization for IGS and ITS Spacer Regions: A Possible Mechanism to Resolve This Paradox

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 243-256 ◽  
Author(s):  
Carlos Polanco ◽  
Ana I González ◽  
Álvaro de la Fuente ◽  
Gabriel A Dover
Keyword(s):  
Drosophila Melanogaster ◽  
Concerted Evolution ◽  
Multigene Family ◽  
Natural Populations ◽  
Intergenic Spacer ◽  
Meiotic Pairing ◽  
Y Chromosomes ◽  
Mutation Distribution ◽  
Chromosome Exchanges

Abstract The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.

scholarly journals Epigenetic Programming of the rRNA Promoter by MBD3

2007 ◽  
Vol 27 (13) ◽  
pp. 4938-4952 ◽  
Author(s):  
Shelley E. Brown ◽  
Moshe Szyf
Keyword(s):  
Small Interfering Rna ◽  
Rna Polymerase I ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Rrna Transcription ◽  
Epigenetic Programming ◽  
Binding Factor ◽  
Upstream Binding Factor ◽  
Polymerase I ◽  
Interfering Rna

ABSTRACT Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

Initiation and termination of DNA replication in human rRNA genes

1993 ◽  
Vol 13 (10) ◽  
pp. 6600-6613
Author(s):  
R D Little ◽  
T H Platt ◽  
C L Schildkraut
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Replication Forks ◽  
Nontranscribed Spacer ◽  
Dna Repeat

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.

Description and phylogenetic analyses of ribosomal transcription units from species of Fasciolidae (Platyhelminthes: Digenea)

2020 ◽  
Vol 94 ◽  
Author(s):  
T.H. Le ◽  
K.L.T. Pham ◽  
H.T.T. Doan ◽  
T.K. Xuyen Le ◽  
K.T. Nguyen ◽  
...  
Keyword(s):  
Fasciola Hepatica ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Transcription Unit ◽  
Rrna Genes ◽  
28S Rrna ◽  
Intergenic Spacer Region ◽  
Repeat Units ◽  
Complete Sequences ◽  
Fasciolopsis Buski

Abstract Many members of Fasciolidae are common trematodes in cattle, buffaloes, sheep, elephants, pigs, with some capable of infecting humans also. In this study, the complete or near-complete sequences of ribosomal transcription unit (rTU or rDNA), each of Fasciola hepatica (Australia), Fascioloides jacksoni (Sri Lanka), Fasciolopsis buski (Vietnam) and three isolates of F. gigantica (Vietnam), were obtained and characterized. The full length of rDNA for each F. hepatica, ‘hybrid’ Fasciola sp., Fas. jacksoni and Fa. Buski, was 7657 bp, 7966 bp, 7781 bp and 8361 bp, with the complete intergenic spacer region (IGS) (862 bp, 1170 bp, 987 bp and 561 bp), respectively. The rDNA of two ‘pure’ F. gigantica isolates from Vietnam was 6794 bp with unsequenced IGS. For 28S rRNA genes the Fasciola spp. are equal, 1958 bp for 18S, 160 bp for 5.8S, 3863 bp and 454 bp for ITS1 but ITS2 differ by one nucleotide (Thymine) (359 or 360 bp). The ITS1 of the sensu lato Fa. buski has some distinguishable features, 286 bp for ITS2, 3862 bp for 28S and four repeat units of 356–361 bp each found in ITS1. The 28S rDNA analysis showed the lowest level of divergence (0–0.57%) between F. hepatica and F. gigantica and higher (2.23–2.62%) and highest (6–6.42%) for Fas. jacksoni and Fasciolopsis, respectively. The tree of 43 strains/species clearly produced a well-supported phylogeny, where 18 fasciolids consistently grouped, forming a discrete Fasciolidae clade, distinct from Philophthalmidae, Echinostomatidae and Echinochasmidae in Echinostomatoidea. Fascioloides jacksoni is outside Fasciola spp.: basal with Fas. magna, as previously demonstrated.

scholarly journals Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array

2009 ◽  
Vol 58 (5) ◽  
pp. 596-605 ◽  
Author(s):  
Siou Cing Su ◽  
Mario Vaneechoutte ◽  
Lenie Dijkshoorn ◽  
Yu Fang Wei ◽  
Ya Lei Chen ◽  
...  
Keyword(s):  
Clinical Importance ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Oligonucleotide Array ◽  
Rrna Genes ◽  
Universal Primers ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nylon Membrane ◽  
Gram Negative

Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S–23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7 %, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.

scholarly journals The cytogenetic boundaries of the rDNA region within heterochromatin of the X chromosome of Drosophila melanogaster and their relation to male meiotic pairing sites

1982 ◽  
Vol 39 (2) ◽  
pp. 149-156 ◽  
Author(s):  
R. Appels ◽  
A. J. Hilliker
Keyword(s):  
Drosophila Melanogaster ◽  
Rrna Genes ◽  
Type I ◽  
28S Rrna ◽  
Meiotic Pairing ◽  
Coding Region ◽  
Intervening Sequences ◽  
Single Region ◽  
Rrna Sequences

SummaryThe proximal breakpoints of the inversion chromosomes In(1)ωm4 and In(1)m51b were shown, by in situ hybridization, to define the boundaries of the ribosomal DNA region located within the X chromosome heterochromatin (Xh). We estimate that at least 95% of the rDNA is located between the In(1)ωm4 and In(1)ωm51b proximal breakpoints. In contrast only 60–70% of the Type I intervening sequences located in Xh are located between these breakpoints. The Type I intervening sequences in the rDNA region occur as inserts in the 28S rRNA sequences while the remainder of the sequences are distal to the In(1)ωm4 breakpoint and not associated with rRNA genes.The regions of Xh which contain rDNA and Type I intervening sequences were related to regions shown by Cooper (1964) to contribute to meiotic pairing between the X and Y chromosomes in male Drosophila. We demonstrate that the rRNA coding region contributes to X / Y pairing. However, no single region of Xh is required for fidelity of male meiotic pairing of the sex chromosomes.

scholarly journals Isolation and characterization of the prune locus of Drosophila melanogaster.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 373-380
Author(s):  
D H Teng ◽  
L B Bender ◽  
C M Engele ◽  
S Tsubota ◽  
T Venkatesh
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Unit ◽  
P Element ◽  
Isolation And Characterization ◽  
Body Tissues ◽  
Length Polymorphisms ◽  
Pigment Biosynthesis ◽  
Adult Head

Abstract The complementary lethal interaction between the prune (pn) and Killer of prune loci of Drosophila melanogaster is an unusual and highly specific phenomenon. A lesion in pn results in a brownish-purple color of the compound eyes, while the conditional dominant Killer of prune mutation exhibits no phenotype by itself. However, a hemizygous or homozygous pn mutant carrying a copy of the Killer of prune gene dies during the late second to third instar stage of larval development. As a step toward understanding the molecular nature of this lethality and the role of pn in pigment biosynthesis, we have cloned the pn locus by using a transposon tag in the P element-induced allele, pn38. In addition, seven independent revertant lines were generated by the remobilization of transposons in pn38. The pn gene is located in a region that is transcriptionally active, and the isolated cDNAs that correspond to this area fall into three transcription units: I, II and III. Southern analysis shows that the restriction fragment length polymorphisms in five pn alleles are localized within a 1.2-kilobase genomic fragment, of which only transcription unit II is a part. The cDNA of this unit recognizes 1.65- and 1.8-kilobase messages in wild-type Drosophila adult head and body tissues that are absent or extremely reduced in pn mutants. Taken together, the results suggest that transcription unit II defines a part of the pn locus and its cDNA encodes a putative structural gene of pn.

Roles of rDNA spacer and transcription unit-sequences in X - Y meiotic chromosome pairing in Drosophila melanogaster males

Chromosoma ◽  
1997 ◽  
Vol 106 (1) ◽  
pp. 29-36 ◽  
Author(s):  
Xiao-jia Ren ◽  
Lynn Eisenhour ◽  
Chia-sin Hong ◽  
Yunsang Lee ◽  
Bruce D. McKee
Keyword(s):  
Drosophila Melanogaster ◽  
Chromosome Pairing ◽  
Meiotic Chromosome ◽  
Transcription Unit ◽  
Meiotic Chromosome Pairing

Molecular cloning and genetic analysis of the suppressor-of-white-apricot locus from Drosophila melanogaster

1987 ◽  
Vol 7 (7) ◽  
pp. 2498-2505
Author(s):  
Z Zachar ◽  
D Garza ◽  
T B Chou ◽  
J Goland ◽  
P M Bingham
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Transfer ◽  
Genetic Analysis ◽  
Developmental Stages ◽  
Chromosomal Region ◽  
Transcription Unit ◽  
Complementation Group ◽  
P Element ◽  
Allele Specific ◽  
New Mutations

We report genetic and molecular analysis of the suppressor-of-white-apricot [su(wa)] locus, one of several retrotransposon insertion allele-specific suppressor loci in Drosophila melanogaster. First, we isolated and characterized eight new mutations allelic to the original su(wa)1 mutation. These studies demonstrated that su(wa) mutations allelic to su(wa)1 affected a conventional D. melanogaster complementation group. Second, we cloned the chromosomal region containing the su(wa) complementation group by P element transposon tagging. The ca. 14-kilobase region surrounding the su(wa) complementation group contained five distinct transcription units, each with a different developmentally programmed pattern of expression. Third, we used a modified procedure for P-mediated gene transfer to identify the transcription unit corresponding to su(wa) by gene transfer. Fourth, we found that the presumptive su(wa) transcription unit produced a family of transcripts (ranging from ca. 3.5 to ca. 5.2 kilobases) in all developmental stages, tissue fractions, and cell lines we examined, suggesting that the gene is universally expressed.

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