Variation in structure and expression of ribosomal DNA loci in wheat

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 963-968 ◽  
Author(s):  
R. B. Flavell
Keyword(s):  
Ribosomal Rna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Gene Methylation ◽  
Regulatory Dna Sequences ◽  
Regulatory Dna ◽  
Inactive Genes ◽  
Rna Genes ◽  
Active Genes

Ribosomal RNA genes are organised in tandem arrays at complex loci called nucleolus organisers. The structure of a locus and of a wheat rRNA gene is described in detail. Active or potentially active genes are in the nucleolus during interphase, while inactive genes are excluded from the nucleolus. Genetic variation exists within a species for the number of the rRNA genes at a locus and also for the structure of the intergenic, regulatory DNA. This variation can affect the activity of a locus, relative to that of another in the same cell and the proportion of the rRNA genes at a locus included in the nucleolus. The active loci are enriched with genes that are not methylated at specific CpG residues in the intergenic regulatory DNA and that are in a chromatin conformation accessible to DNase I. A model is presented that attempts to relate the structural variation between genes to the differential expression and nucleolar organisation of the rRNA genes at different loci. The model is based on the affinity of proteins, in limiting concentration, to specific regulatory DNA sequences. These sequences are subject to change as a result of mechanisms that can spread mutations through a locus. The resulting variation, which may not be eliminated by selection unless it is very deleterious and accounts for a large part of the total rDNA, may be one reason why plants maintain a large excess of ribosomal RNA genes.Key words: nucleolus, ribosomal RNA gene, methylation.

Basonuclin is associated with the ribosomal RNA genes on human keratinocyte mitotic chromosomes

1999 ◽  
Vol 112 (18) ◽  
pp. 3039-3047 ◽  
Author(s):  
H. Tseng ◽  
J.A. Biegel ◽  
R.S. Brown
Keyword(s):  
Ribosomal Rna ◽  
Zinc Fingers ◽  
Hair Follicles ◽  
Ribosomal Rna Genes ◽  
Rrna Genes ◽  
Control Element ◽  
Rrna Gene ◽  
Metaphase Chromosomes ◽  
Acrocentric Chromosomes ◽  
Rna Genes

Basonuclin is a zinc finger protein mainly expressed in keratinocytes of the basal layer of epidermis and the outer root sheath of hair follicles. It is also found in abundance in the germ cells of testis and ovary. In cultured keratinocytes, basonuclin is associated with chromatin in all phases of the cell cycle, including mitosis. By immunocytochemical methods, we demonstrate here that in mitosis basonuclin is associated with the short arms of the acrocentric chromosomes and with other loci on many metaphase chromosomes of human keratinocytes. Using the evolutionarily highly conserved N-terminal pair of zinc fingers in an electrophoresis mobility shift assay, we demonstrate that the DNA target sequences of basonuclin on the acrocentric chromosomes are likely to be within the promoter region of the 45S rRNA gene transcription unit. DNase I footprinting shows that basonuclin zinc fingers interact with the upstream control element of this promoter, which is necessary for the high level of transcription of the rRNA genes. This result suggests that basonuclin may be a tissue-specific transcription factor for the ribosomal RNA genes.

scholarly journals Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events.

Genetics ◽  
1990 ◽  
Vol 126 (4) ◽  
pp. 875-888 ◽  
Author(s):  
S M Newman ◽  
J E Boynton ◽  
N W Gillham ◽  
B L Randolph-Anderson ◽  
A M Johnson ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Chloroplast Genome ◽  
Ribosomal Rna ◽  
Dna Sequences ◽  
Inverted Repeat ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Complete Replacement ◽  
Biolistic Process

Abstract Transformation of chloroplast ribosomal RNA (rRNA) genes in Chlamydomonas has been achieved by the biolistic process using cloned chloroplast DNA fragments carrying mutations that confer antibiotic resistance. The sites of exchange employed during the integration of the donor DNA into the recipient genome have been localized using a combination of antibiotic resistance mutations in the 16S and 23S rRNA genes and restriction fragment length polymorphisms that flank these genes. Complete or nearly complete replacement of a region of the chloroplast genome in the recipient cell by the corresponding sequence from the donor plasmid was the most common integration event. Exchange events between the homologous donor and recipient sequences occurred preferentially near the vector:insert junctions. Insertion of the donor rRNA genes and flanking sequences into one inverted repeat of the recipient genome was followed by intramolecular copy correction so that both copies of the inverted repeat acquired identical sequences. Increased frequencies of rRNA gene transformants were achieved by reducing the copy number of the chloroplast genome in the recipient cells and by decreasing the heterology between donor and recipient DNA sequences flanking the selectable markers. In addition to producing bona fide chloroplast rRNA transformants, the biolistic process induced mutants resistant to low levels of streptomycin, typical of nuclear mutations in Chlamydomonas.

Expressed retrotransposed 5S rRNA genes in the mouse and rat genomes

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 213-215 ◽  
Author(s):  
Guy Drouin
Keyword(s):  
Key Words ◽  
Ribosomal Rna ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
5S Ribosomal Rna ◽  
Gene Copies ◽  
5S Rrna Gene ◽  
5S Rrna Genes ◽  
Rna Genes

The analyses of previously described 5S rRNA gene sequences show that some of the expressed 5S rRNA genes present in the mouse and rat genomes were derived from the retrotransposition of 5S rRNA transcripts. These analyses demonstrate that new 5S rRNA gene copies can originate by retrotransposition and that some of these retrotranscribed genes are expressed. Key words: 5S ribosomal RNA genes, retrotransposition, retroposons.

scholarly journals Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene

2018 ◽  
Author(s):  
Kami Ahmad ◽  
Amy E Spens
Keyword(s):  
Dna Sequences ◽  
Target Genes ◽  
Chromatin Modification ◽  
Chromatin Domains ◽  
Response Elements ◽  
Regulatory Dna Sequences ◽  
Polycomb Response Elements ◽  
Regulatory Dna ◽  
Inactive Genes ◽  
Endogenous Locus

Patterned expression of many developmental genes is specified by transcription factor gene expression, but is thought to be refined by chromatin-mediated repression. Regulatory DNA sequences called Polycomb Response Elements (PREs) are required to repress some developmental target genes, and are widespread in genomes, suggesting that they broadly affect developmental programs. While PREs in transgenes can nucleate trimethylation on lysine 27 of the histone H3 tail (H3K27me3), none have been demonstrated to be necessary at endogenous chromatin domains. This failure is thought to be due to the fact that most endogenous H3K27me3 domains contain many PREs, and individual PREs may be redundant. In contrast to these ideas, we show here that PREs near the wing selector gene vestigial have distinctive roles at their endogenous locus, even though both PREs are repressors in transgenes. First, a PRE near the promoter is required for vestigial activation and not for repression. Second, only the distal PRE contributes to H3K27me3, but even removal of both PREs does not eliminate H3K27me3 across the vestigial domain. Thus, endogenous chromatin domains appear to be intrinsically marked by H3K27me3, and PREs appear required to enhance this chromatin modification to high levels at inactive genes.

scholarly journals Three Redescriptions in Tintinnopsis (Protista ：Ciliophora: Tintinnina) from Coastal Waters of China, with Cytology and Phylogenetic Analyses Based on Ribosomal RNA Genes

2020 ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background: The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods.Results: Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) genes were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originating from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa.Conclusion: The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary pattern and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

scholarly journals Characterization, Comparative Analysis and Phylogenetic Implications of Mitogenomes of Fulgoridae (Hemiptera: Fulgoromorpha)

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1185
Author(s):  
Wenqian Wang ◽  
Huan Zhang ◽  
Jérôme Constant ◽  
Charles R. Bartlett ◽  
Daozheng Qin
Keyword(s):  
Control Region ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Start Codon ◽  
Rrna Genes ◽  
Rich Region ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Rna Genes ◽  
Unpaired Base

The complete mitogenomes of nine fulgorid species were sequenced and annotated to explore their mitogenome diversity and the phylogenetics of Fulgoridae. All species are from China and belong to five genera: Dichoptera Spinola, 1839 (Dichoptera sp.); Neoalcathous Wang and Huang, 1989 (Neoalcathous huangshanana Wang and Huang, 1989); Limois Stål, 1863 (Limois sp.); Penthicodes Blanchard, 1840 (Penthicodes atomaria (Weber, 1801), Penthicodes caja (Walker, 1851), Penthicodes variegata (Guérin-Méneville, 1829)); Pyrops Spinola, 1839 (Pyrops clavatus (Westwood, 1839), Pyrops lathburii (Kirby, 1818), Pyrops spinolae (Westwood, 1842)). The nine mitogenomes were 15,803 to 16,510 bp in length with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (A + T-rich region). Combined with previously reported fulgorid mitogenomes, all PCGs initiate with either the standard start codon of ATN or the nonstandard GTG. The TAA codon was used for termination more often than the TAG codon and the incomplete T codon. The nad1 and nad4 genes varied in length within the same genus. A high percentage of F residues were found in the nad4 and nad5 genes of all fulgorid mitogenomes. The DHU stem of trnV was absent in the mitogenomes of all fulgorids sequenced except Dichoptera sp. Moreover, in most fulgorid mitogenomes, the trnL2, trnR, and trnT genes had an unpaired base in the aminoacyl stem and trnS1 had an unpaired base in the anticodon stem. The similar tandem repeat regions of the control region were found in the same genus. Phylogenetic analyses were conducted based on 13 PCGs and two rRNA genes from 53 species of Fulgoroidea and seven outgroups. The Bayesian inference and maximum likelihood trees had a similar topological structure. The major results show that Fulgoroidea was divided into two groups: Delphacidae and ((Achilidae + (Lophopidae + (Issidae + (Flatidae + Ricaniidae)))) + Fulgoridae). Furthermore, the monophyly of Fulgoridae was robustly supported, and Aphaeninae was divided into Aphaenini and Pyropsini, which includes Neoalcathous, Pyrops, Datua Schmidt, 1911, and Saiva Distant, 1906. The genus Limois is recovered in the Aphaeninae, and the Limoisini needs further confirmation; Dichoptera sp. was the earliest branch in the Fulgoridae.

scholarly journals Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

2020 ◽  
Author(s):  
Abigail Hui En Chan ◽  
Kittipong Chaisiri ◽  
Serge Morand ◽  
Naowarat Saralamba ◽  
Urusa Thaenkham
Keyword(s):  
Genetic Marker ◽  
Genetic Markers ◽  
Molecular Systematics ◽  
Ribosomal Rna ◽  
Ribosomal Rna Genes ◽  
16S Ribosomal Rna ◽  
12S Rrna ◽  
Rrna Gene ◽  
12S Rrna Gene ◽  
Rna Genes

Abstract Background Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. Methods To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. Results The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. Conclusions This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

scholarly journals Three redescriptions in Tintinnopsis (Protista: Ciliophora: Tintinnina) from coastal waters of China, with cytology and phylogenetic analyses based on ribosomal RNA genes

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yang Bai ◽  
Rui Wang ◽  
Wen Song ◽  
Lifang Li ◽  
Luciana F. Santoferrara ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Coastal Waters ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Middle Portion ◽  
Closely Related Species ◽  
Molecular Information ◽  
Ciliary Tuft ◽  
Rna Genes ◽  
Rrna Sequences

Abstract Background The taxonomy of tintinnine ciliates is vastly unresolved because it has traditionally been based on the lorica (a secreted shell) and it has only recently incorporated cytological and molecular information. Tintinnopsis, the most speciose tintinnine genus, is also the most problematic: it is known to be non-monophyletic, but it cannot be revised until more of its species are studied with modern methods. Results Here, T. hemispiralis Yin, 1956, T. kiaochowensis Yin, 1956, and T. uruguayensis Balech, 1948, from coastal waters of China, were studied. Lorica and cell features were morphometrically investigated in living and protargol-stained specimens, and sequences of three ribosomal RNA (rRNA) loci were phylogenetically analyzed. The three species show a complex ciliary pattern (with ventral, dorsal, and posterior kineties and right, left, and lateral ciliary fields), but differ in lorica morphology, details of the somatic ciliature and rRNA gene sequences. Tintinnopsis hemispiralis is further distinguished by a ciliary tuft (a ribbon of very long cilia originated from the middle portion of the ventral kinety and extending out of the lorica) and multiple macronuclear nodules. Both T. kiaochowensis and T. uruguayensis have two macronuclear nodules, but differ in the number of somatic kineties and the position of the posterior kinety. Two neotypes are fixed for T. hemispiralis and T. kiaochowensis to stabilize the species names objectively, mainly because of the previous unavailability of type materials. By phylogenetic analysis and comparison with closely-related species, we infer that the ciliary tuft and details such as the commencement of the rightmost kinety in the lateral ciliary field are synapomorphies that may help clarify the systematics of Tintinnopsis-like taxa. Conclusion The redescriptions of three poorly known Tintinnopsis species, namely T. hemispiralis, T. kiaochowensis, and T. uruguayensis firstly revealed their ciliary patterns and rRNA sequences. This study expands knowledge and database of tintinnines and helps in identifying potential synapomorphies for future taxonomic rearrangements.

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